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3j7h

Structure of beta-galactosidase at 3.2-A resolution obtained by cryo-electron microscopy

Method: ELECTRON MICROSCOPY Dmax: 173.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Beta-galactosidase

OrganismNot specified

UniProt P00722

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–1024 Chain B； UniProt 1–1024 Chain C； UniProt 1–1024 Chain D； UniProt 1–1024 Not recorded MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：25 mM Tris, pH 8.0, 50 mM NaCl, 2 mM MgCl2, 0.5 mM TCEP；pH 8；25 mM Tris, pH 8.0, 50 mM NaCl, 2 mM MgCl2, 0.5 mM TCEP cryo-EM vitrification conditions：Blot for 2 seconds before plunging.；90.15 K；Cryogen ETHANE；Blot for 2 seconds before plunging into liquid ethane (LEICA EM GP). Resolution 3.20 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3J7H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DP0 E. COLI BETA-GALACTOSIDASE AT 1.7 ANGSTROM Deposited 1999-12-22 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 9–1023（1015 aa）
Chain B 9–1023（1015 aa）
Chain C 9–1023（1015 aa）
Chain D 9–1023（1015 aa）
Not recorded MG MAGNESIUM ION × 16 NA SODIUM ION × 20 DMS DIMETHYL SULFOXIDE × 112 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；10 % PEG 8000 100 MM BIS-TRIS 200 MM MGCL(2) 100 MM NACL 10 MM DTT, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 1.70 Å R-free 0.211
1F4A E. COLI (LACZ) BETA-GALACTOSIDASE (NCS CONSTRAINED MONOMER-ORTHORHOMBIC) Deposited 2000-06-07 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 3–1023（1021 aa）
Chain B 3–1023（1021 aa）
Chain C 3–1023（1021 aa）
Chain D 3–1023（1021 aa）
Not recorded MG MAGNESIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；10% PEG 2KMME, 100 mM Bis-Tris, 200 mM MgCl(2), 1 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.198
1F4H E. COLI (LACZ) BETA-GALACTOSIDASE (ORTHORHOMBIC) Deposited 2000-06-07 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 3–1023（1021 aa）
Chain B 3–1023（1021 aa）
Chain C 3–1023（1021 aa）
Chain D 3–1023（1021 aa）
Not recorded MG MAGNESIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；10 % PEG 2KMME, 100 mM Bis-Tris, 200 mM MgCl(2), 1 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.279
1HN1 E. COLI (LAC Z) BETA-GALACTOSIDASE (ORTHORHOMBIC) Deposited 2000-12-05 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 9–1023（1015 aa）
Chain B 9–1023（1015 aa）
Chain C 9–1023（1015 aa）
Chain D 9–1023（1015 aa）
Not recorded MG MAGNESIUM ION × 8 NA SODIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；10% PEG 8000, 100 mM BIS TRIS, 200 mM MGCL(2), 100 mM NACL, 10 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 3.00 Å R-free 0.299
1JYN E. COLI (lacZ) BETA-GALACTOSIDASE (E537Q) IN COMPLEX WITH LACTOSE Deposited 2001-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Mutation：E537Q Mutation：E537Q Mutation：E537Q Mutation：E537Q MG MAGNESIUM ION × 14 NA SODIUM ION × 15 DMS DIMETHYL SULFOXIDE × 96 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；PEG 8000, NaCl, MgCl2, DTT, Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50
Resolution 1.80 Å R-free 0.219
1JYV E. COLI (lacZ) BETA-GALACTOSIDASE (E537Q) IN COMPLEX WITH ONPG Deposited 2001-09-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Mutation：E537Q Mutation：E537Q Mutation：E537Q Mutation：E537Q MG MAGNESIUM ION × 17 NA SODIUM ION × 16 145 2-nitrophenyl beta-D-galactopyranoside × 8 DMS DIMETHYL SULFOXIDE × 107 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；BIS-TRIS, PEG 8000, MGCL(2), NACL, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50
Resolution 1.75 Å R-free 0.240
1JYW E. COLI (lacZ) BETA-GALACTOSIDASE (E537Q) IN COMPLEX WITH PNPG Deposited 2001-09-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Mutation：E537Q Mutation：E537Q Mutation：E537Q Mutation：E537Q 147 4-nitrophenyl beta-D-galactopyranoside × 4 MG MAGNESIUM ION × 15 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 109 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50
Resolution 1.55 Å R-free 0.229
1JYX E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH IPTG Deposited 2001-09-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Not recorded MG MAGNESIUM ION × 9 NA SODIUM ION × 14 IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 6 DMS DIMETHYL SULFOXIDE × 74 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50
Resolution 1.75 Å R-free 0.244
1JZ2 E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-F-GALACTOSYL-ENZYME INTERMEDIATE (ORTHORHOMBIC) Deposited 2001-09-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Not recorded 2FG 2-deoxy-2-fluoro-beta-D-galactopyranose × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 12 DMS DIMETHYL SULFOXIDE × 69 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50
Resolution 2.10 Å R-free 0.270
1JZ3 E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL ENZYME INTERMEDIATE Deposited 2001-09-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Not recorded 2DG 2-deoxy-alpha-D-galactopyranose × 4 MG MAGNESIUM ION × 17 NA SODIUM ION × 16 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 DMS DIMETHYL SULFOXIDE × 110 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50
Resolution 1.75 Å R-free 0.222
1JZ4 E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL-ENZYME INTERMEDIATE (Low Bis-Tris) Deposited 2001-09-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Not recorded 2DG 2-deoxy-alpha-D-galactopyranose × 4 MG MAGNESIUM ION × 10 NA SODIUM ION × 15 DMS DIMETHYL SULFOXIDE × 103 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50
Resolution 2.10 Å R-free 0.267
1JZ5 E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH D-GALCTOPYRANOSYL-1-ON Deposited 2001-09-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Not recorded 149 D-galactonolactone × 4 MG MAGNESIUM ION × 11 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 87 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50
Resolution 1.80 Å R-free 0.231
1JZ6 E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH GALACTO-TETRAZOLE Deposited 2001-09-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Not recorded GTZ (5R, 6S, 7S, 8S)-5-HYDROXYMETHYL-6,7,8-TRIHYDROXY-TETRAZOLO[1,5-A]PIPERIDINE × 4 MG MAGNESIUM ION × 13 NA SODIUM ION × 11 DMS DIMETHYL SULFOXIDE × 74 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50
Resolution 2.10 Å R-free 0.270
1JZ7 E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH GALACTOSE Deposited 2001-09-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GAL beta-D-galactopyranose × 8 MG MAGNESIUM ION × 15 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 91 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50
Resolution 1.50 Å R-free 0.219
1JZ8 E. COLI (lacZ) BETA-GALACTOSIDASE (E537Q) IN COMPLEX WITH ALLOLACTOSE Deposited 2001-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Mutation：E537Q Mutation：E537Q Mutation：E537Q Mutation：E537Q MG MAGNESIUM ION × 16 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 127 BGC beta-D-glucopyranose × 1 TAR D(-)-TARTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50
Resolution 1.50 Å R-free 0.208
1PX3 E. COLI (LACZ) BETA-GALACTOSIDASE (G794A) Deposited 2003-07-02 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 9–1023（1015 aa）
Chain B 9–1023（1015 aa）
Chain C 9–1023（1015 aa）
Chain D 9–1023（1015 aa）
Mutation：G794A Mutation：G794A Mutation：G794A Mutation：G794A MG MAGNESIUM ION × 12 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 85 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；PEG 8000, NACL, MGCL2, DTT, BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 1.60 Å R-free 0.243
1PX4 E. COLI (LACZ) BETA-GALACTOSIDASE (G794A) WITH IPTG BOUND Deposited 2003-07-02 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 9–1023（1015 aa）
Chain B 9–1023（1015 aa）
Chain C 9–1023（1015 aa）
Chain D 9–1023（1015 aa）
Mutation：G794A Mutation：G794A Mutation：G794A Mutation：G794A MG MAGNESIUM ION × 16 NA SODIUM ION × 16 IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 4 DMS DIMETHYL SULFOXIDE × 94 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；PEG 8000, NACL, MGCL2, DTT, BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 1.60 Å R-free 0.239
28YO Beta-galactosidase from E.Coli Deposited 2026-03-02 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Mutation：F1008L Mutation：F1008L Mutation：F1008L Mutation：F1008L No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.48 Å
3CZJ E. COLI (lacZ) BETA-GALACTOSIDASE (N460T) IN COMPLEX WITH D-GALCTOPYRANOSYL-1-ONE Deposited 2008-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 10–1024（1015 aa）
Chain B 10–1024（1015 aa）
Chain D 10–1024（1015 aa）
Mutation：N461T Mutation：N461T Mutation：N461T 149 D-galactonolactone × 3 MG MAGNESIUM ION × 7 NA SODIUM ION × 12 DMS DIMETHYL SULFOXIDE × 69 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；PEG 8000, NaCl, MgCl2, DTT, Bis-Tris, pH 6.5, HANGING DROP at 288K, pH 6.50, VAPOR DIFFUSION, HANGING DROP
Resolution 2.05 Å R-free 0.231
3CZJ E. COLI (lacZ) BETA-GALACTOSIDASE (N460T) IN COMPLEX WITH D-GALCTOPYRANOSYL-1-ONE Deposited 2008-04-29 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa）
Chain B 10–1024（1015 aa）
Chain C 10–1024（1015 aa）
Chain D 10–1024（1015 aa）
Mutation：N461T Mutation：N461T Mutation：N461T Mutation：N461T 149 D-galactonolactone × 4 MG MAGNESIUM ION × 9 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 94 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；PEG 8000, NaCl, MgCl2, DTT, Bis-Tris, pH 6.5, HANGING DROP at 288K, pH 6.50, VAPOR DIFFUSION, HANGING DROP
Resolution 2.05 Å R-free 0.231
3DYM E. coli (lacZ) beta-galactosidase (H418E) Deposited 2008-07-28 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa）
Chain B 10–1024（1015 aa）
Chain C 10–1024（1015 aa）
Chain D 10–1024（1015 aa）
Mutation：H418E Mutation：H418E Mutation：H418E Mutation：H418E MG MAGNESIUM ION × 10 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 82 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.05 Å R-free 0.251
3DYO E. coli (lacZ) beta-galactosidase (H418N) in complex with IPTG Deposited 2008-07-28 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa）
Chain B 10–1024（1015 aa）
Chain C 10–1024（1015 aa）
Chain D 10–1024（1015 aa）
Mutation：H418N Mutation：H418N Mutation：H418N Mutation：H418N MG MAGNESIUM ION × 14 NA SODIUM ION × 18 IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 12 DMS DIMETHYL SULFOXIDE × 97 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 1.80 Å R-free 0.241
3DYP E. coli (lacZ) beta-galactosidase (H418N) Deposited 2008-07-28 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa）
Chain B 10–1024（1015 aa）
Chain C 10–1024（1015 aa）
Chain D 10–1024（1015 aa）
Mutation：H418N Mutation：H418N Mutation：H418N Mutation：H418N MG MAGNESIUM ION × 16 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 107 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 1.75 Å R-free 0.217
3E1F E.Coli (lacZ) beta-galactosidase (H418E) in complex with galactose Deposited 2008-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain 1 10–1024（1015 aa） Fragment：BETA-GALACTOSIDASE
Chain 2 10–1024（1015 aa） Fragment：BETA-GALACTOSIDASE
Chain 3 10–1024（1015 aa） Fragment：BETA-GALACTOSIDASE
Chain 4 10–1024（1015 aa） Fragment：BETA-GALACTOSIDASE
Mutation：H418E Mutation：H418E Mutation：H418E Mutation：H418E MG MAGNESIUM ION × 10 NA SODIUM ION × 13 DMS DIMETHYL SULFOXIDE × 73 GAL beta-D-galactopyranose × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50
Resolution 3.00 Å R-free 0.249
3SEP E. coli (lacZ) beta-galactosidase (S796A) Deposited 2011-06-10 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain B 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain C 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain D 10–1024（1015 aa） Fragment：Unp residues 10-1024
Mutation：S796A Mutation：S796A Mutation：S796A Mutation：S796A MG MAGNESIUM ION × 9 NA SODIUM ION × 14 DMS DIMETHYL SULFOXIDE × 78 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；8-10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Resolution 2.05 Å R-free 0.221
3T08 E. coli (LacZ) beta-galactosidase (S796A) IPTG complex Deposited 2011-07-19 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain B 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain C 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain D 10–1024（1015 aa） Fragment：Unp residues 10-1024
Mutation：S796A Mutation：S796A Mutation：S796A Mutation：S796A MG MAGNESIUM ION × 9 NA SODIUM ION × 13 IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 4 DMS DIMETHYL SULFOXIDE × 71 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；8-10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Resolution 2.00 Å R-free 0.223
3T09 E. coli (LacZ) beta-galactosidase (S796A) galactonolactone complex Deposited 2011-07-19 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain B 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain C 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain D 10–1024（1015 aa） Fragment：Unp residues 10-1024
Mutation：S796A Mutation：S796A Mutation：S796A Mutation：S796A 149 D-galactonolactone × 4 MG MAGNESIUM ION × 11 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 107 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；8-10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Resolution 1.75 Å R-free 0.254
3T0A E. coli (LacZ) beta-galactosidase (S796T) Deposited 2011-07-19 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain B 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain C 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain D 10–1024（1015 aa） Fragment：Unp residues 10-1024
Mutation：S796T Mutation：S796T Mutation：S796T Mutation：S796T MG MAGNESIUM ION × 12 NA SODIUM ION × 17 DMS DIMETHYL SULFOXIDE × 110 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；8-10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Resolution 1.90 Å R-free 0.214
3T0B E. coli (LacZ) beta-galactosidase (S796T) IPTG complex Deposited 2011-07-19 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain B 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain C 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain D 10–1024（1015 aa） Fragment：Unp residues 10-1024
Mutation：S796T Mutation：S796T Mutation：S796T Mutation：S796T MG MAGNESIUM ION × 8 NA SODIUM ION × 14 IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 4 DMS DIMETHYL SULFOXIDE × 69 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；8-10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Resolution 2.40 Å R-free 0.233
3T0D E.coli (lacZ) beta-galactosidase (S796T) in complex with galactonolactone Deposited 2011-07-20 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain B 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain C 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain D 10–1024（1015 aa） Fragment：Unp residues 10-1024
Mutation：S796T Mutation：S796T Mutation：S796T Mutation：S796T 149 D-galactonolactone × 4 MG MAGNESIUM ION × 9 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 104 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；8-10% PEG 8000, 100 mM Bis-tris, 200 mM MgCl2, 100 mM NaCl, 10 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Resolution 1.93 Å R-free 0.209
3T2O E. coli (lacZ) beta-galactosidase (S796D) Deposited 2011-07-22 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain B 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain C 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain D 10–1024（1015 aa） Fragment：Unp residues 10-1024
Mutation：S796D Mutation：S796D Mutation：S796D Mutation：S796D MG MAGNESIUM ION × 16 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 112 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；8-10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Resolution 1.85 Å R-free 0.182
3T2P E. coli (lacZ) beta-galactosidase (S796D) in complex with IPTG Deposited 2011-07-22 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain B 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain C 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain D 10–1024（1015 aa） Fragment：Unp residues 10-1024
Mutation：S796D Mutation：S796D Mutation：S796D Mutation：S796D IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 10 DMS DIMETHYL SULFOXIDE × 63 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；8-10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Resolution 2.60 Å R-free 0.242
3T2Q E. coli (lacZ) beta-galactosidase (S796D) in complex with galactonolactone Deposited 2011-07-22 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain B 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain C 10–1024（1015 aa） Fragment：Unp residues 10-1024
Chain D 10–1024（1015 aa） Fragment：Unp residues 10-1024
Mutation：S796D Mutation：S796D Mutation：S796D Mutation：S796D 149 D-galactonolactone × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 11 DMS DIMETHYL SULFOXIDE × 49 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；8-10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Resolution 2.40 Å R-free 0.239
3VD3 E. coli (lacZ) beta-galactosidase (N460D) Deposited 2012-01-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa）
Chain B 10–1024（1015 aa）
Chain C 10–1024（1015 aa）
Chain D 10–1024（1015 aa）
Mutation：N460D Mutation：N460D Mutation：N460D Mutation：N460D MG MAGNESIUM ION × 7 NA SODIUM ION × 12 DMS DIMETHYL SULFOXIDE × 45 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；10% PEG8000, 100 mM Bis-Tris, pH 6.5, 200 mM magnesium chloride, 100 mM sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.80 Å R-free 0.282
3VD4 E. coli (lacZ) beta-galactosidase (N460D) in complex with IPTG Deposited 2012-01-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa）
Chain B 10–1024（1015 aa）
Chain C 10–1024（1015 aa）
Chain D 10–1024（1015 aa）
Mutation：N460D Mutation：N460D Mutation：N460D Mutation：N460D MG MAGNESIUM ION × 9 NA SODIUM ION × 14 DMS DIMETHYL SULFOXIDE × 68 IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；10% PEG8000, 100 mM Bis-Tris, pH 6.5, 200 mM magnesium chloride, 100 mM sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.00 Å R-free 0.212
3VD5 E. coli (lacZ) beta-galactosidase (N460S) Deposited 2012-01-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa）
Chain B 10–1024（1015 aa）
Chain C 10–1024（1015 aa）
Chain D 10–1024（1015 aa）
Mutation：N460S Mutation：N460S Mutation：N460S Mutation：N460S MG MAGNESIUM ION × 8 NA SODIUM ION × 11 DMS DIMETHYL SULFOXIDE × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；10% PEG8000, 100 mM Bis-Tris, pH 6.5, 200 mM magnesium chloride, 100 mM sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.70 Å R-free 0.276
3VD7 E. coli (lacZ) beta-galactosidase (N460S) in complex with galactotetrazole Deposited 2012-01-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa）
Chain B 10–1024（1015 aa）
Chain C 10–1024（1015 aa）
Chain D 10–1024（1015 aa）
Mutation：N460S Mutation：N460S Mutation：N460S Mutation：N460S GTZ (5R, 6S, 7S, 8S)-5-HYDROXYMETHYL-6,7,8-TRIHYDROXY-TETRAZOLO[1,5-A]PIPERIDINE × 4 MG MAGNESIUM ION × 6 NA SODIUM ION × 8 DMS DIMETHYL SULFOXIDE × 29 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；10% PEG8000, 100 mM Bis-Tris, pH 6.5, 200 mM magnesium chloride, 100 mM sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.87 Å R-free 0.250
3VD9 E. coli (lacZ) beta-galactosidase (N460S) in complex with IPTG Deposited 2012-01-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa）
Chain B 10–1024（1015 aa）
Chain C 10–1024（1015 aa）
Chain D 10–1024（1015 aa）
Mutation：N460S Mutation：N460S Mutation：N460S Mutation：N460S MG MAGNESIUM ION × 9 NA SODIUM ION × 16 IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 4 DMS DIMETHYL SULFOXIDE × 64 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；10% PEG8000, 100 mM Bis-Tris, pH 6.5, 200 mM magnesium chloride, 100 mM sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.05 Å R-free 0.223
3VDA E. coli (lacZ) beta-galactosidase (N460T) Deposited 2012-01-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa）
Chain B 10–1024（1015 aa）
Chain C 10–1024（1015 aa）
Chain D 10–1024（1015 aa）
Mutation：N460T Mutation：N460T Mutation：N460T Mutation：N460T MG MAGNESIUM ION × 8 NA SODIUM ION × 10 DMS DIMETHYL SULFOXIDE × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；10% PEG8000, 100 mM Bis-Tris, pH 6.5, 200 mM magnesium chloride, 100 mM sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.50 Å R-free 0.237
3VDB E. coli (lacZ) beta-galactosidase (N460T) in complex with galactonolactone Deposited 2012-01-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa）
Chain B 10–1024（1015 aa）
Chain C 10–1024（1015 aa）
Chain D 10–1024（1015 aa）
Mutation：N460T Mutation：N460T Mutation：N460T Mutation：N460T 149 D-galactonolactone × 4 MG MAGNESIUM ION × 9 NA SODIUM ION × 14 DMS DIMETHYL SULFOXIDE × 77 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；10% PEG8000, 100 mM Bis-Tris, pH 6.5, 200 mM magnesium chloride, 100 mM sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.05 Å R-free 0.205
3VDC E. coli (lacZ) beta-galactosidase (N460T) in complex with IPTG Deposited 2012-01-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa）
Chain B 10–1024（1015 aa）
Chain C 10–1024（1015 aa）
Chain D 10–1024（1015 aa）
Mutation：N460T Mutation：N460T Mutation：N460T Mutation：N460T IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 10 DMS DIMETHYL SULFOXIDE × 46 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；10% PEG8000, 100 mM Bis-Tris, pH 6.5, 200 mM magnesium chloride, 100 mM sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.55 Å R-free 0.236
4CKD Model of complex between the E.coli enzyme beta-galactosidase and four single chain Fv antibody domains scFv13R4. Deposited 2014-01-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20% PHOSPHATE BUFFERED SALINE (PBS)；pH 7.4；20% PHOSPHATE BUFFERED SALINE (PBS)
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 100, INSTRUMENT- OTHER, METHOD- BLOT FOR 10-20 SECONDS UNTIL DIAMETER OF BLOTTED MENISCUS CEASES TO EXPAND, BEFORE PLUNGING.
Resolution 13.00 Å
4DUV E. coli (lacZ) beta-galactosidase (G974A) 2-deoxy-galactosyl-enzyme and bis-Tris complex Deposited 2012-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa） Fragment：unp residues 10-1024
Chain B 10–1024（1015 aa） Fragment：unp residues 10-1024
Chain C 10–1024（1015 aa） Fragment：unp residues 10-1024
Chain D 10–1024（1015 aa） Fragment：unp residues 10-1024
Mutation：G794A Mutation：G794A Mutation：G794A Mutation：G794A 2DG 2-deoxy-alpha-D-galactopyranose × 4 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 MG MAGNESIUM ION × 9 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 90 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.10 Å R-free 0.206
4DUW E. coli (lacZ) beta-galactosidase (G974A) in complex with allolactose Deposited 2012-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa） Fragment：unp residues 10-1024
Chain B 10–1024（1015 aa） Fragment：unp residues 10-1024
Chain C 10–1024（1015 aa） Fragment：unp residues 10-1024
Chain D 10–1024（1015 aa） Fragment：unp residues 10-1024
Mutation：G794A Mutation：G794A Mutation：G794A Mutation：G794A MG MAGNESIUM ION × 10 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 77 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.20 Å R-free 0.213
4DUX E. coli (lacZ) beta-galactosidase (N460S) in complex with L-ribose Deposited 2012-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–1024（1015 aa） Fragment：unp residues 10-1024
Chain B 10–1024（1015 aa） Fragment：unp residues 10-1024
Chain C 10–1024（1015 aa） Fragment：unp residues 10-1024
Chain D 10–1024（1015 aa） Fragment：unp residues 10-1024
Mutation：N460S Mutation：N460S Mutation：N460S Mutation：N460S 0MK beta-L-ribopyranose × 9 MG MAGNESIUM ION × 8 NA SODIUM ION × 14 DMS DIMETHYL SULFOXIDE × 65 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.30 Å R-free 0.221
4V40 BETA-GALACTOSIDASE Deposited 1994-07-18 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Not recorded MG MAGNESIUM ION × 8 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
4V40 BETA-GALACTOSIDASE Deposited 1994-07-18 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 1–1023（1023 aa）
Chain F 1–1023（1023 aa）
Chain G 1–1023（1023 aa）
Chain H 1–1023（1023 aa）
Not recorded MG MAGNESIUM ION × 8 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
4V40 BETA-GALACTOSIDASE Deposited 1994-07-18 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain I 1–1023（1023 aa）
Chain J 1–1023（1023 aa）
Chain K 1–1023（1023 aa）
Chain L 1–1023（1023 aa）
Not recorded MG MAGNESIUM ION × 8 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
4V40 BETA-GALACTOSIDASE Deposited 1994-07-18 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain M 1–1023（1023 aa）
Chain N 1–1023（1023 aa）
Chain O 1–1023（1023 aa）
Chain P 1–1023（1023 aa）
Not recorded MG MAGNESIUM ION × 7 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
4V41 E. COLI (LAC Z) BETA-GALACTOSIDASE (NCS CONSTRAINED MONOMER-MONOCLINIC) Deposited 2000-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；PEG 8000, Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Resolution 2.50 Å R-free 0.207
4V41 E. COLI (LAC Z) BETA-GALACTOSIDASE (NCS CONSTRAINED MONOMER-MONOCLINIC) Deposited 2000-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 1–1023（1023 aa）
Chain F 1–1023（1023 aa）
Chain G 1–1023（1023 aa）
Chain H 1–1023（1023 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；PEG 8000, Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Resolution 2.50 Å R-free 0.207
4V41 E. COLI (LAC Z) BETA-GALACTOSIDASE (NCS CONSTRAINED MONOMER-MONOCLINIC) Deposited 2000-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain I 1–1023（1023 aa）
Chain J 1–1023（1023 aa）
Chain K 1–1023（1023 aa）
Chain L 1–1023（1023 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；PEG 8000, Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Resolution 2.50 Å R-free 0.207
4V41 E. COLI (LAC Z) BETA-GALACTOSIDASE (NCS CONSTRAINED MONOMER-MONOCLINIC) Deposited 2000-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain M 1–1023（1023 aa）
Chain N 1–1023（1023 aa）
Chain O 1–1023（1023 aa）
Chain P 1–1023（1023 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；PEG 8000, Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Resolution 2.50 Å R-free 0.207
4V44 E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH 2-F-LACTOSE Deposited 2001-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 8 NA SODIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；295 K；Cacodylate, PEG 8000, MgSO4, NaCl, BME, pH 5.9, VAPOR DIFFUSION, HANGING DROP at 295K, pH 5.90
Resolution 2.70 Å
4V44 E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH 2-F-LACTOSE Deposited 2001-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 1–1023（1023 aa）
Chain F 1–1023（1023 aa）
Chain G 1–1023（1023 aa）
Chain H 1–1023（1023 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 8 NA SODIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；295 K；Cacodylate, PEG 8000, MgSO4, NaCl, BME, pH 5.9, VAPOR DIFFUSION, HANGING DROP at 295K, pH 5.90
Resolution 2.70 Å
4V44 E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH 2-F-LACTOSE Deposited 2001-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain I 1–1023（1023 aa）
Chain J 1–1023（1023 aa）
Chain K 1–1023（1023 aa）
Chain L 1–1023（1023 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 8 NA SODIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；295 K；Cacodylate, PEG 8000, MgSO4, NaCl, BME, pH 5.9, VAPOR DIFFUSION, HANGING DROP at 295K, pH 5.90
Resolution 2.70 Å
4V44 E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH 2-F-LACTOSE Deposited 2001-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain M 1–1023（1023 aa）
Chain N 1–1023（1023 aa）
Chain O 1–1023（1023 aa）
Chain P 1–1023（1023 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 8 NA SODIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；295 K；Cacodylate, PEG 8000, MgSO4, NaCl, BME, pH 5.9, VAPOR DIFFUSION, HANGING DROP at 295K, pH 5.90
Resolution 2.70 Å
4V45 E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-F-GALACTOSYL-ENZYME INTERMEDIATE Deposited 2001-09-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1023（1023 aa）
Chain B 1–1023（1023 aa）
Chain C 1–1023（1023 aa）
Chain D 1–1023（1023 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 2FG 2-deoxy-2-fluoro-beta-D-galactopyranose × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；295 K；Cacodylate, PEG 8000, MgSO4, NaCl, BME, pH 5.9, VAPOR DIFFUSION, HANGING DROP at 295K, pH 5.90
Resolution 2.60 Å
4V45 E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-F-GALACTOSYL-ENZYME INTERMEDIATE Deposited 2001-09-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 1–1023（1023 aa）
Chain F 1–1023（1023 aa）
Chain G 1–1023（1023 aa）
Chain H 1–1023（1023 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 2FG 2-deoxy-2-fluoro-beta-D-galactopyranose × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；295 K；Cacodylate, PEG 8000, MgSO4, NaCl, BME, pH 5.9, VAPOR DIFFUSION, HANGING DROP at 295K, pH 5.90
Resolution 2.60 Å
4V45 E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-F-GALACTOSYL-ENZYME INTERMEDIATE Deposited 2001-09-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain I 1–1023（1023 aa）
Chain J 1–1023（1023 aa）
Chain K 1–1023（1023 aa）
Chain L 1–1023（1023 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 2FG 2-deoxy-2-fluoro-beta-D-galactopyranose × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；295 K；Cacodylate, PEG 8000, MgSO4, NaCl, BME, pH 5.9, VAPOR DIFFUSION, HANGING DROP at 295K, pH 5.90
Resolution 2.60 Å
4V45 E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-F-GALACTOSYL-ENZYME INTERMEDIATE Deposited 2001-09-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain M 1–1023（1023 aa）
Chain N 1–1023（1023 aa）
Chain O 1–1023（1023 aa）
Chain P 1–1023（1023 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 2FG 2-deoxy-2-fluoro-beta-D-galactopyranose × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；295 K；Cacodylate, PEG 8000, MgSO4, NaCl, BME, pH 5.9, VAPOR DIFFUSION, HANGING DROP at 295K, pH 5.90
Resolution 2.60 Å
5A1A 2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor Deposited 2015-04-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 3–1024（1022 aa）
Chain B 3–1024（1022 aa）
Chain C 3–1024（1022 aa）
Chain D 3–1024（1022 aa）
Not recorded PTQ 2-phenylethyl 1-thio-beta-D-galactopyranoside × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM TRIS, PH 8.0, 50 MM NACL, 2 MM MGCL2, 0.5 MM TCEP；pH 8；25 MM TRIS, PH 8.0, 50 MM NACL, 2 MM MGCL2, 0.5 MM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；BLOT FOR 2 SECONDS BEFORE PLUNGING INTO LIQUID ETHANE (LEICA EM GP).
Resolution 2.20 Å
6CVM Atomic resolution cryo-EM structure of beta-galactosidase Deposited 2018-03-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 3–1023（1021 aa）
Chain B 3–1023（1021 aa）
Chain C 3–1023（1021 aa）
Chain D 3–1023（1021 aa）
Not recorded PTQ 2-phenylethyl 1-thio-beta-D-galactopyranoside × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25 mM Tris, pH 8.0, 50 mM NaCl, 2 mM MgCl2, 1.0 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 2 seconds before plunging.
Resolution 1.90 Å
6DRV Beta-galactosidase Deposited 2018-06-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
6KUZ E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSL01 Deposited 2019-09-03 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Mutation：E537Q Mutation：E537Q DVL 3-(1,3-benzothiazol-2-yl)-2-[[4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]methoxy]-5-methyl-benzaldehyde × 4 NA SODIUM ION × 12 DMS DIMETHYL SULFOXIDE × 42 MG MAGNESIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；291 K；10% PEG8000, 100mM Bis-Tris ph5,9, 200mM Nacl, 10mM DTT, 0.1M Guanidine Hydrochloride 10% glycerol
Resolution 2.83 Å R-free 0.224
6KUZ E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSL01 Deposited 2019-09-03 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Mutation：E537Q Mutation：E537Q DVL 3-(1,3-benzothiazol-2-yl)-2-[[4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]methoxy]-5-methyl-benzaldehyde × 4 NA SODIUM ION × 12 DMS DIMETHYL SULFOXIDE × 28 MG MAGNESIUM ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；291 K；10% PEG8000, 100mM Bis-Tris ph5,9, 200mM Nacl, 10mM DTT, 0.1M Guanidine Hydrochloride 10% glycerol
Resolution 2.83 Å R-free 0.224
6X1Q 1.8 Angstrom resolution structure of b-galactosidase with a 200 kV cryoARM electron microscope Deposited 2020-05-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 3–1023（1021 aa）
Chain B 3–1023（1021 aa）
Chain C 3–1023（1021 aa）
Chain D 3–1023（1021 aa）
Not recorded MG MAGNESIUM ION × 8 NA SODIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25mM Tris pH 8.0, 50mM NaCl, 0.5mM TCEP, 2mM MgCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.80 Å
7BRS E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA02 Deposited 2020-03-30 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Mutation：E537Q Mutation：E537Q F4X 8-[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-indol-1-ium-1-yl]octanoic acid × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 6 DMS DIMETHYL SULFOXIDE × 54 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；100mM Bis-Tris, pH=5.9, 200mM NaCl, 200mM MgCl2, 10% PEG8000, 10% glycerol, 0.1M guanidine hydrochloride, 10mM DTT
Resolution 2.67 Å R-free 0.244
7BRS E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA02 Deposited 2020-03-30 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Mutation：E537Q Mutation：E537Q F4X 8-[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-indol-1-ium-1-yl]octanoic acid × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 8 DMS DIMETHYL SULFOXIDE × 38 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；100mM Bis-Tris, pH=5.9, 200mM NaCl, 200mM MgCl2, 10% PEG8000, 10% glycerol, 0.1M guanidine hydrochloride, 10mM DTT
Resolution 2.67 Å R-free 0.244
7BTK E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA01 Deposited 2020-04-01 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Mutation：E537Q Mutation：E537Q F6L 4-[[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-2H-indol-1-yl]methyl]benzoic acid × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 8 DMS DIMETHYL SULFOXIDE × 40 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；100 mM Bis-Tris, pH = 5.9, 200 mM NaCl, 200 mM MgCl2, 10% PEG8000, 10% glycerol, 0.1 M guanidine hydrochloride and 10 mM DTT
Resolution 2.70 Å R-free 0.233
7BTK E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA01 Deposited 2020-04-01 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Mutation：E537Q Mutation：E537Q F6L 4-[[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-2H-indol-1-yl]methyl]benzoic acid × 4 MG MAGNESIUM ION × 6 NA SODIUM ION × 6 DMS DIMETHYL SULFOXIDE × 36 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；100 mM Bis-Tris, pH = 5.9, 200 mM NaCl, 200 mM MgCl2, 10% PEG8000, 10% glycerol, 0.1 M guanidine hydrochloride and 10 mM DTT
Resolution 2.70 Å R-free 0.233
8BK7 Cryo-EM structure of beta-galactosidase at 3.3 A resolution plunged 5 ms after mixing with apoferritin Deposited 2022-11-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；contains Amaranth dye (acid red 27) 32 mM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8BK8 Cryo-EM structure of beta-galactosidase at 2.9 A resolution plunged 205 ms after mixing with apoferritin Deposited 2022-11-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；contains Amaranth dye (acid red 27) 32 mM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8BKG Cryo-EM structure of beta-galactosidase at 3.2 A resolution plunged 35 ms after mixing with apoferritin Deposited 2022-11-09 Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；contains Amaranth dye (acid red 27) 32 mM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Q7Y ESIBD structure of beta-galactosidase Deposited 2023-08-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.9；Soft-landed sample
cryo-EM vitrification conditions Cryogen OTHER；Soft-landed as described in manuscript
Resolution 2.60 Å
8RI6 Beta-galactosidase (LacZ) purified from E. coli. Deposited 2023-12-18 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Not recorded MG MAGNESIUM ION × 8 NA SODIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25 mM Tris, 50 mM NaCl, 2 mM MgCl2, 2 mM EDTA, 1 mM TCEP, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.06 Å
8RI7 Beta-galactosidase (LacZ) in complex with glycosyrin from Pseudomonas syringae. Deposited 2023-12-18 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Not recorded A1H05 (2S,3R,4S)-2-[bis(oxidanyl)methyl]pyrrolidine-3,4-diol × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25 mM Tris, 50 mM NaCl, 2 mM MgCl2, 2 mM EDTA, 1 mM TCEP, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.93 Å
8RI8 Beta-galactosidase (LacZ) in complex with synthetic glycosyrin. Deposited 2023-12-18 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Not recorded A1H05 (2S,3R,4S)-2-[bis(oxidanyl)methyl]pyrrolidine-3,4-diol × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25 mM Tris, 50 mM NaCl, 2 mM MgCl2, 2 mM EDTA, 1 mM TCEP, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.42 Å
9HKI Plunge-frozen beta-galactosidase Deposited 2024-12-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 3–1023（1021 aa）
Chain B 3–1023（1021 aa）
Chain C 3–1023（1021 aa）
Chain D 3–1023（1021 aa）
Not recorded MG MAGNESIUM ION × 4 NA SODIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；25 mM Tris (pH 7.9), 50 mM NaCl, 10 mM EDTA, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 1.90 Å
9HLM Soft-landed and rehydrated beta-galactosidase (best particles) Deposited 2024-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 3–1023（1021 aa）
Chain B 3–1023（1021 aa）
Chain C 3–1023（1021 aa）
Chain D 3–1023（1021 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
Resolution 3.70 Å
9HPL E. coli beta-galactosidase labeled with Chromeo P503 dye purified using MISO Deposited 2024-12-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25 mM HEPES pH 8.0, 100 mM NaCl, 500 mM imidazole and 1mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9HPM E. coli beta-galactosidase labeled with Chromeo P503 dye purified using MISO from 1ug Deposited 2024-12-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25 mM HEPES pH 8.0, 100 mM NaCl, 500 mM imidazole and 1mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9Y45 His-tagged beta galactosidase (LacZ) on a Ni-NTA lipid monolayer grid Deposited 2025-09-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1024（1024 aa）
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Chain D 1–1024（1024 aa）
Not recorded MG MAGNESIUM ION × 8 NA SODIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.41 Å

67 other PDB entries and 83 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BGAL_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1024； UniProt 1–1024 Author chain B； PDBConstruct 1–1024； UniProt 1–1024 Author chain C； PDBConstruct 1–1024； UniProt 1–1024 Author chain D； PDBConstruct 1–1024； UniProt 1–1024

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3j7h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3j7h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3j7h
Deposition date deposition_date2014-06-30
Structure title titleStructure of beta-galactosidase at 3.2-A resolution obtained by cryo-electron microscopy
Keywords keywords;hydrolase enzyme, homo-tetramer, protein complex, atomic resolution cryo-electron microscopy, direct electron detectors, single-particle cryo-EM, 3D reconstruction, HYDROLASE ;; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier52.23 Å
Radius of gyration Rg (electron density) rg_electron51.91 Å
Forward intensity I(0) i03214570000.00
Molecular weight molecular_weight464870.0 kDa
Excluded volume excluded_volume575980 ų
Envelope volume envelope_volume752840 ų
Hydration-shell volume shell_volume116160 ų
Envelope diameter envelope_diameter183.6 Å
Shell Rg shell_rg59.10 Å
Envelope Rg envelope_rg51.14 Å
Shape Rg shape_rg51.88 Å
Total Rg total_rg52.18 Å
Total atoms total_atoms32828
Residues n_residues4088
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax173.5 Å
Rg (real space) rg_real52.14 Å
Rg uncertainty (real space) rg_real_error1.38 Å
I(0) (real space) i0_real3.2150e+09
I(0) uncertainty (real space) i0_real_error6.1360e+07
Rg (reciprocal space) rg_reciprocal52.30 Å
I(0) (reciprocal space) i0_reciprocal3215000000.0000
Solution quality estimate total_estimate0.8674
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary63.6 Å
Skewness Skewness skewness0.301
Kurtosis Kurtosis kurtosis-0.200
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha593600000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.758
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

Domain ID domain_id3j7hA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id3j7hA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3j7hA03
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id3j7hA04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3j7hA05
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3j7hB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id3j7hB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3j7hB03
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id3j7hB04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3j7hB05
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3j7hC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id3j7hC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3j7hC03
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id3j7hC04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3j7hC05
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3j7hD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id3j7hD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3j7hD03
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id3j7hD04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3j7hD05
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)