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2y5p

B-repeat of Listeria monocytogenes InlB (internalin B)

Method: X-RAY DIFFRACTION Dmax: 85.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

INTERNALIN B

LISTERIA MONOCYTOGENES EGD

UniProt P25147

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 322–392 Fragment：B-REPEAT, RESIDUES 322-392 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 2 UL PROTEIN (17.3 MG/ML) PLUS 1 UL RESERVOIR (0.1 M NA-ACETATE PH 5.0, 0.2 M CACL2, 18 % PEG 6000). Resolution 1.30 Å R-free 0.196
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 322–392 Fragment：B-REPEAT, RESIDUES 322-392 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 2 UL PROTEIN (17.3 MG/ML) PLUS 1 UL RESERVOIR (0.1 M NA-ACETATE PH 5.0, 0.2 M CACL2, 18 % PEG 6000). Resolution 1.30 Å R-free 0.196
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 322–392 Fragment：B-REPEAT, RESIDUES 322-392 CA CALCIUM ION × 3 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 2 UL PROTEIN (17.3 MG/ML) PLUS 1 UL RESERVOIR (0.1 M NA-ACETATE PH 5.0, 0.2 M CACL2, 18 % PEG 6000). Resolution 1.30 Å R-free 0.196
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 322–392 Fragment：B-REPEAT, RESIDUES 322-392 CA CALCIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 2 UL PROTEIN (17.3 MG/ML) PLUS 1 UL RESERVOIR (0.1 M NA-ACETATE PH 5.0, 0.2 M CACL2, 18 % PEG 6000). Resolution 1.30 Å R-free 0.196
5 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 322–392 Chain B； UniProt 322–392 Chain C； UniProt 322–392 Chain D； UniProt 322–392 Fragment：B-REPEAT, RESIDUES 322-392 CA CALCIUM ION × 8 CL CHLORIDE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 2 UL PROTEIN (17.3 MG/ML) PLUS 1 UL RESERVOIR (0.1 M NA-ACETATE PH 5.0, 0.2 M CACL2, 18 % PEG 6000). Resolution 1.30 Å R-free 0.196

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 2Y5P Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D0B INTERNALIN B LEUCINE RICH REPEAT DOMAIN Deposited 1999-09-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–248（213 aa） Fragment：LRR DOMAIN, RESIDUES 36-248
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM MES, 200 mM Calcium Acetate, 20% PEG 8000, 1 mM DTT , pH 6.5, vapor diffusion, temperature 298K
Resolution 1.86 Å R-free 0.235
1H6T Internalin B: crystal structure of fused N-terminal domains. Deposited 2001-06-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–321（286 aa） Fragment：LRR DOMAIN, RESIDUES 36-321
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；293 K；0.2M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 5.0, 13% W/V PEG 4000, 6% V/V 2-METHYL-2,4-PENTANDIOL, T=20C, PROTEIN CONC.=10 MG/ML
Resolution 1.60 Å R-free 0.197
1M9S Crystal structure of Internalin B (InlB), a Listeria monocytogenes virulence protein containing SH3-like domains. Deposited 2002-07-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–630（595 aa）
Not recorded TB TERBIUM(III) ION × 7 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；lithium sulfate, glycerol, dithiothreitol, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.65 Å R-free 0.302
1OTM Calcium-binding mutant of the internalin B LRR domain Deposited 2003-03-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–248（213 aa） Fragment：LRR domain
Mutation：D51A, D59A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Peg 8000, Mes, Calcium acetate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.93 Å R-free 0.240
1OTN Calcium-binding mutant of the Internalin B LRR domain Deposited 2003-03-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–248（213 aa） Fragment：LRR domain
Mutation：D51A CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Peg 8000, Mes, Calcium acetate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.97 Å R-free 0.244
1OTO Calcium-binding mutant of the internalin B LRR domain Deposited 2003-03-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–248（213 aa） Fragment：LRR domain
Mutation：D59A CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Peg 8000, Mes, Calcium acetate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.96 Å R-free 0.230
2UZX Structure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein InlB: Crystal form I Deposited 2007-05-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–321（286 aa） Fragment：INTERNALIN DOMAIN (CAP, LRR, IR), INLB321, RESIDUES 36-320
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 DEG C VAPOR DIFFUSION. 2 UL PROTEIN (5 MG/ML) PLUS 1 UL RESERVOIR CONSISTING OF 16.5% PEG 1500, 4.4% MPD, 0.1 M TRIS, PH8.5. RESERVOIR WAS COVERED WITH ALS OIL.
Resolution 2.80 Å R-free 0.307
2UZX Structure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein InlB: Crystal form I Deposited 2007-05-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 36–321（286 aa） Fragment：INTERNALIN DOMAIN (CAP, LRR, IR), INLB321, RESIDUES 36-320
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 DEG C VAPOR DIFFUSION. 2 UL PROTEIN (5 MG/ML) PLUS 1 UL RESERVOIR CONSISTING OF 16.5% PEG 1500, 4.4% MPD, 0.1 M TRIS, PH8.5. RESERVOIR WAS COVERED WITH ALS OIL.
Resolution 2.80 Å R-free 0.307
2UZY Structure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein inlb: low resolution, Crystal form II Deposited 2007-05-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–321（286 aa） Fragment：INTERNALIN DOMAIN (CAP, LRR, IR)\: INLB321, RESIDUES 36-321
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；VAPOR DIFFUSION AT 25 DEGREE C IN SITTING-DROPS. 2 UL PROTEIN (8 MG/ML)PLUS 2 UL RESERVOIR (1.4 M NA/K PHOSPHATE, PH 6.5, 10% PEG 2000 MONO-METHYL-ETHER)
Resolution 4.00 Å R-free 0.301
2UZY Structure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein inlb: low resolution, Crystal form II Deposited 2007-05-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 36–321（286 aa） Fragment：INTERNALIN DOMAIN (CAP, LRR, IR)\: INLB321, RESIDUES 36-321
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；VAPOR DIFFUSION AT 25 DEGREE C IN SITTING-DROPS. 2 UL PROTEIN (8 MG/ML)PLUS 2 UL RESERVOIR (1.4 M NA/K PHOSPHATE, PH 6.5, 10% PEG 2000 MONO-METHYL-ETHER)
Resolution 4.00 Å R-free 0.301
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form Deposited 2009-08-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.
Resolution 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form Deposited 2009-08-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.
Resolution 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form Deposited 2009-08-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.
Resolution 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form Deposited 2009-08-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.
Resolution 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form Deposited 2009-08-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.
Resolution 2.60 Å R-free 0.249
2WQU Internalin domain of Listeria monocytogenes InlB: triclinic crystal form Deposited 2009-08-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.
Resolution 2.60 Å R-free 0.249
2WQV Internalin domain of Listeria monocytogenes InlB: rhombohedral crystal form Deposited 2009-08-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；SITTING VAPOR DIFFUSION AT 293 K. 200 NL PROTEIN PLUS 100 NL OF RESERVOIR SOLUTION CONSISTING OF 0.1 M NACL, 0.1 M CHES PH 9.5, 40% PEG300. THE PROTEIN WAS ACTUALLY A COMPLEX OF MET741 WITH INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG/ML. CRYSTAL GROWTH TIME: SEVERAL WEEKS TO MONTHS.
Resolution 2.80 Å R-free 0.238
2WQV Internalin domain of Listeria monocytogenes InlB: rhombohedral crystal form Deposited 2009-08-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；SITTING VAPOR DIFFUSION AT 293 K. 200 NL PROTEIN PLUS 100 NL OF RESERVOIR SOLUTION CONSISTING OF 0.1 M NACL, 0.1 M CHES PH 9.5, 40% PEG300. THE PROTEIN WAS ACTUALLY A COMPLEX OF MET741 WITH INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG/ML. CRYSTAL GROWTH TIME: SEVERAL WEEKS TO MONTHS.
Resolution 2.80 Å R-free 0.238
2WQW DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER of the Listeria monocytogenes InlB internalin domain Deposited 2009-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Mutation：YES PEG DI(HYDROXYETHYL)ETHER × 12 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9.5；293 K；293 K. PROTEIN (6.7 MG/ML) PLUS RESERVOIR = 2 PLUS 1. RESERVOIR SOLUTION IS 44-52% PEG2000, 0.1 M CHES PH=9,5, 0.2M NACL., PH 9.5
Resolution 2.24 Å R-free 0.239
2WQW DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER of the Listeria monocytogenes InlB internalin domain Deposited 2009-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Mutation：YES PEG DI(HYDROXYETHYL)ETHER × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9.5；293 K；293 K. PROTEIN (6.7 MG/ML) PLUS RESERVOIR = 2 PLUS 1. RESERVOIR SOLUTION IS 44-52% PEG2000, 0.1 M CHES PH=9,5, 0.2M NACL., PH 9.5
Resolution 2.24 Å R-free 0.239
2WQX InlB321_4R: S199R, D200R, G206R, A227R, C242A mutant of the Listeria monocytogenes InlB internalin domain Deposited 2009-08-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP VAPOUR DIFFUSION AT 293K WITH 1 UL PROTEIN (3.8 MG/ML IN 50 MM HEPES, PH 7.0, 100 MM NACL) PLUS 0.5 UL RESERVOIR (17% PEG1000MME, 90 MM NA-CITRATE).
Resolution 2.03 Å R-free 0.257
2WQX InlB321_4R: S199R, D200R, G206R, A227R, C242A mutant of the Listeria monocytogenes InlB internalin domain Deposited 2009-08-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–321（286 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP VAPOUR DIFFUSION AT 293K WITH 1 UL PROTEIN (3.8 MG/ML IN 50 MM HEPES, PH 7.0, 100 MM NACL) PLUS 0.5 UL RESERVOIR (17% PEG1000MME, 90 MM NA-CITRATE).
Resolution 2.03 Å R-free 0.257
2Y5Q Listeria monocytogenes InlB (internalin B) residues 36-392 Deposited 2011-01-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–392（357 aa） Fragment：INTERNALIN DOMAIN AND B-REPEAT, RESIDUES 36-392
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 1.5 UL PROTEIN (5 MG/ML) PLUS 1.5 UL RESERVOIR (0.1 M MES, PH 5.5, 14 % MPD) MICROSEEDED FROM A SIMILAR CONDITION (0.1 M MES PH 6.0, 6.5 % PEG6000 AND 5 MM ZNCL2).
Resolution 3.20 Å R-free 0.225
2Y5Q Listeria monocytogenes InlB (internalin B) residues 36-392 Deposited 2011-01-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–392（357 aa） Fragment：INTERNALIN DOMAIN AND B-REPEAT, RESIDUES 36-392
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 DEG C IN HANGING OR SITTING-DROPS WITH 1.5 UL PROTEIN (5 MG/ML) PLUS 1.5 UL RESERVOIR (0.1 M MES, PH 5.5, 14 % MPD) MICROSEEDED FROM A SIMILAR CONDITION (0.1 M MES PH 6.0, 6.5 % PEG6000 AND 5 MM ZNCL2).
Resolution 3.20 Å R-free 0.225
4AW4 Engineered variant of Listeria monocytogenes InlB internalin domain with an additional leucine rich repeat inserted Deposited 2012-05-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–98（63 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Chain A 99–321（223 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Not recorded SO4 SULFATE ION × 9 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP VAPOUR DIFFUSION IN 96-WELL PLATES AT 20 DEGREE C. 17 MG/ML PROTEIN IN 25 MM TRIS, PH 8, 20 MM NACL. RESERVOIR SOLUTION WAS 2M AMMONIUM SULFATE. DROPS WERE SET UP WITH EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION.
Resolution 1.93 Å R-free 0.205
4AW4 Engineered variant of Listeria monocytogenes InlB internalin domain with an additional leucine rich repeat inserted Deposited 2012-05-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–98（63 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Chain B 99–321（223 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Not recorded SO4 SULFATE ION × 7 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP VAPOUR DIFFUSION IN 96-WELL PLATES AT 20 DEGREE C. 17 MG/ML PROTEIN IN 25 MM TRIS, PH 8, 20 MM NACL. RESERVOIR SOLUTION WAS 2M AMMONIUM SULFATE. DROPS WERE SET UP WITH EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION.
Resolution 1.93 Å R-free 0.205
4AW4 Engineered variant of Listeria monocytogenes InlB internalin domain with an additional leucine rich repeat inserted Deposited 2012-05-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 36–98（63 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Chain C 99–321（223 aa） Fragment：INTERNALIN DOMAIN, RESIDUES 36-321
Not recorded SO4 SULFATE ION × 6 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SITTING DROP VAPOUR DIFFUSION IN 96-WELL PLATES AT 20 DEGREE C. 17 MG/ML PROTEIN IN 25 MM TRIS, PH 8, 20 MM NACL. RESERVOIR SOLUTION WAS 2M AMMONIUM SULFATE. DROPS WERE SET UP WITH EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION.
Resolution 1.93 Å R-free 0.205
4CIL YopM-InlB: Hybrid leucine-rich repeat protein Deposited 2013-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 93–321（229 aa） Fragment：YOPM N-TERMINAL CAP RESIDUES 34-87, INLB LEUCINE-RICH REPEAT AND INTER-REPEAT REGION RESIDUES 93-321
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HANGING DROP VAPOUR DIFFUSION AT 293 K WITH A DROP SIZE OF 2 UL CONSISTING OF EQUAL VOLUMES OF PROTEIN AT A CONCENTRATION OF 10 MG/ML AND RESERVOIR SOLUTION (0.1 M TRICINE, PH 9.0, 28% PEG 1000, 10% GLYCEROL, 0.25M KCL). CRYSTALS WERE CRYO-PROTECTED WITH RESERVOIR-SOLUTION ADDITIONALLY CONTAINING 15% GLYCEROL AND FLASH-FROZEN IN LIQUID NITROGEN
Resolution 1.50 Å R-free 0.219
6GCU MET receptor in complex with InlB internalin domain and DARPin A3A Deposited 2018-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 36–321（286 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1 M HEPES sodium salt pH 7.5, 12% w/v PEG4000, protein complex concentration 5 mg/mL, equimolar ratio of macromolecules, drop size 0.2 uL, protein:reservoir ratio 1:1
Resolution 6.00 Å R-free 0.271
6GCU MET receptor in complex with InlB internalin domain and DARPin A3A Deposited 2018-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 36–321（286 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1 M HEPES sodium salt pH 7.5, 12% w/v PEG4000, protein complex concentration 5 mg/mL, equimolar ratio of macromolecules, drop size 0.2 uL, protein:reservoir ratio 1:1
Resolution 6.00 Å R-free 0.271

16 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INLB_LISMO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–74； UniProt 322–392 Author chain B； PDBConstruct 4–74； UniProt 322–392 Author chain C； PDBConstruct 4–74； UniProt 322–392 Author chain D； PDBConstruct 4–74； UniProt 322–392

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 2y5p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2y5p
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2y5p
Deposition date deposition_date2011-01-17
Structure title titleB-repeat of Listeria monocytogenes InlB (internalin B)
Keywords keywordsPROTEIN BINDING, VIRULENCE FACTOR, PATHOGENICITY FACTOR, BETA-GRASP FOLD; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.06 Å
Radius of gyration Rg (electron density) rg_electron25.60 Å
Forward intensity I(0) i018271600.00
Molecular weight molecular_weight33099.0 kDa
Excluded volume excluded_volume41575 ų
Envelope volume envelope_volume53178 ų
Hydration-shell volume shell_volume19241 ų
Envelope diameter envelope_diameter87.3 Å
Shell Rg shell_rg30.08 Å
Envelope Rg envelope_rg25.80 Å
Shape Rg shape_rg25.59 Å
Total Rg total_rg26.23 Å
Total atoms total_atoms2324
Residues n_residues289
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 dmax85.3 Å
Rg (real space) rg_real26.36 Å
Rg uncertainty (real space) rg_real_error0.63 Å
I(0) (real space) i0_real1.8270e+07
I(0) uncertainty (real space) i0_real_error2.5170e+05
Rg (reciprocal space) rg_reciprocal26.27 Å
I(0) (reciprocal space) i0_reciprocal18270000.0000
Solution quality estimate total_estimate0.8358
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.8 Å
Skewness Skewness skewness0.564
Kurtosis Kurtosis kurtosis-0.352
Angular range angular_range— – 0.3050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2538000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.732; Smooth: 0.707
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id2y5pA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily4270 — Listeria-Bacteroides repeat domain
Domain ID domain_id2y5pB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily4270 — Listeria-Bacteroides repeat domain
Domain ID domain_id2y5pC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily4270 — Listeria-Bacteroides repeat domain
Domain ID domain_id2y5pD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily4270 — Listeria-Bacteroides repeat domain
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8. Citations (1)

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9. Files and Curves (10)