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3dfo

Dihydroxyacetone phosphate Schiff base and enamine intermediates in D33N mutant fructose-1,6-bisphosphate aldolase from rabbit muscle

Method: X-RAY DIFFRACTION Dmax: 112.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Fructose-bisphosphate aldolase A

Oryctolagus cuniculus

UniProt P00883

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 2–364 Chain B； UniProt 2–364 Chain C； UniProt 2–364 Chain D； UniProt 2–364 Mutation：D33N 13P 1,3-DIHYDROXYACETONEPHOSPHATE × 4 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；296 K；sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K, pH 7.50 Resolution 1.94 Å R-free 0.199

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 3DFO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
11NH Rabbit muscle Aldolase (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 0x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon
Resolution 2.42 Å
11NI Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon in the presence of 0x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon
Resolution 2.27 Å
11NJ Rabbit muscle Aldolase (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 0.25x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon
Resolution 2.40 Å
11NK Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon in the presence of 0.25x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon
Resolution 2.17 Å
11NL Rabbit muscle Aldolase (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 0.5x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon
Resolution 2.41 Å
11NM Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon in the presence of 0.5x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon
Resolution 2.19 Å
11NN Rabbit muscle Aldolase (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon
Resolution 2.34 Å
11NO Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon
Resolution 2.10 Å
11NP Rabbit muscle Aldolase (C1 symmetry) determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon
Resolution 2.43 Å
11NR Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon
Resolution 2.17 Å
11NT Rabbit muscle Aldolase (C1 symmetry) determined using the TFS Vitrobot Mark IV in the presence of 0x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the TFS Vitrobot Mark IV
Resolution 2.25 Å
11NU Rabbit muscle Aldolase (D2 symmetry) determined using the TFS Vitrobot Mark IV in the presence of 0x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the TFS Vitrobot Mark IV
Resolution 1.97 Å
11NW Rabbit muscle Aldolase (C1 symmetry) determined using the TFS Vitrobot Mark IV in the presence of 1x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the TFS Vitrobot Mark IV
Resolution 2.16 Å
11NX Rabbit muscle Aldolase (D2 symmetry) determined using the TFS Vitrobot Mark IV in the presence of 1x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the TFS Vitrobot Mark IV
Resolution 1.98 Å
11OB Rabbit muscle Aldolase (C1 symmetry) determined using a manually-operated plunging device in the presence of 0.25x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Samples were frozen using a manually-operated plunging device
Resolution 2.38 Å
11OC Rabbit muscle Aldolase (D2 symmetry) determined using a manually-operated plunging device in the presence of 0.25x SurfACT Deposited 2026-03-05 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Samples were frozen using a manually-operated plunging device
Resolution 2.18 Å
1ADO FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE FROM RABBIT MUSCLE Deposited 1996-12-02 Different construct 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 1–363（363 aa）
Chain B 1–363（363 aa）
Chain C 1–363（363 aa）
Chain D 1–363（363 aa）
Not recorded 13P 1,3-DIHYDROXYACETONEPHOSPHATE × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；RABBIT MUSCLE ALDOLASE WAS CRYSTALLIZED FROM A 42% SATURATED AMMONIUM SULFATE SOLUTION, pH 7.5
Resolution 1.90 Å R-free 0.203
1EWD FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE FROM RABBIT MUSCLE Deposited 2000-04-25 Different construct 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 1–363（363 aa）
Chain B 1–363（363 aa）
Chain C 1–363（363 aa）
Chain D 1–363（363 aa）
Mutation：K107M Mutation：K107M Mutation：K107M Mutation：K107M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions SMALL TUBES；pH 7.4；293 K；Ammonium sulfate 43%, EDTA 5mM, TRIETHYLAMINE 100mM, pH 7.4, SMALL TUBES, temperature 293K
Resolution 2.46 Å R-free 0.234
1EWE Fructose 1,6-Bisphosphate Aldolase from Rabbit Muscle Deposited 2000-04-25 Different construct 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 1–363（363 aa）
Chain B 1–363（363 aa）
Chain C 1–363（363 aa）
Chain D 1–363（363 aa）
Mutation：K107M Mutation：K107M Mutation：K107M Mutation：K107M SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions SMALL TUBES；pH 7.4；293 K；Ammonium sulfate, 43 percent 5mM EDTA, pH 7.4, SMALL TUBES, temperature 293K
Resolution 2.60 Å R-free 0.237
1EX5 FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE FROM RABBIT MUSCLE Deposited 2000-04-25 Different construct 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 1–363（363 aa）
Chain B 1–363（363 aa）
Chain C 1–363（363 aa）
Chain D 1–363（363 aa）
Mutation：E187A Mutation：E187A Mutation：E187A Mutation：E187A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions SMALL TUBES；pH 7.4；293 K；40% ammonium sulphate, 5mM EDTA, pH 7.4, SMALL TUBES, temperature 293K
Resolution 2.20 Å R-free 0.229
1J4E FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE COVALENTLY BOUND TO THE SUBSTRATE DIHYDROXYACETONE PHOSPHATE Deposited 2001-09-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–363（363 aa）
Chain B 1–363（363 aa）
Chain C 1–363（363 aa）
Chain D 1–363（363 aa）
Mutation：C72A, C239A, C289A, C338A Mutation：C72A, C239A, C289A, C338A Mutation：C72A, C239A, C289A, C338A Mutation：C72A, C239A, C289A, C338A 13P 1,3-DIHYDROXYACETONEPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；pH 7.4
Resolution 2.65 Å R-free 0.249
1ZAH Fructose-1,6-bisphosphate aldolase from rabbit muscle Deposited 2005-04-06 Different construct 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 1–363（363 aa）
Chain B 1–363（363 aa）
Chain C 1–363（363 aa）
Chain D 1–363（363 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.80 Å R-free 0.205
1ZAI Fructose-1,6-bisphosphate Schiff base intermediate in FBP aldolase from rabbit muscle Deposited 2005-04-06 Different construct 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 1–363（363 aa）
Chain B 1–363（363 aa）
Chain C 1–363（363 aa）
Chain D 1–363（363 aa）
Not recorded 2FP 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM) × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.76 Å R-free 0.190
1ZAJ Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with mannitol-1,6-bisphosphate, a competitive inhibitor Deposited 2005-04-06 Different construct 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 1–363（363 aa）
Chain B 1–363（363 aa）
Chain C 1–363（363 aa）
Chain D 1–363（363 aa）
Not recorded M2P D-MANNITOL-1,6-DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.89 Å R-free 0.204
1ZAL Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with partially disordered tagatose-1,6-bisphosphate, a weak competitive inhibitor Deposited 2005-04-06 Different construct 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 1–363（363 aa）
Chain B 1–363（363 aa）
Chain C 1–363（363 aa）
Chain D 1–363（363 aa）
Not recorded PO4 PHOSPHATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.89 Å R-free 0.211
2OT0 Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with a C-terminal peptide of Wiskott-Aldrich syndrome protein Deposited 2007-02-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；HEPES, MgCl2, PEG 550 MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.05 Å R-free 0.200
2OT1 Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with naphthol AS-E phosphate, a competitive inhibitor Deposited 2007-02-07 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded N3P N-(4-CHLOROPHENYL)-3-(PHOSPHONOOXY)NAPHTHALENE-2-CARBOXAMIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.05 Å R-free 0.197
2QUT Dihydroxyacetone phosphate enamine intermediate in fructose-1,6-bisphosphate aldolase from rabbit muscle Deposited 2007-08-06 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded 13P 1,3-DIHYDROXYACETONEPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.88 Å R-free 0.191
2QUU Dihydroxyacetone phosphate Schiff base intermediate in mutant fructose-1,6-bisphosphate aldolase from rabbit muscle Deposited 2007-08-06 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Mutation：K146M Mutation：K146M Mutation：K146M Mutation：K146M 13P 1,3-DIHYDROXYACETONEPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.98 Å R-free 0.195
2QUV Phosphate ions in fructose-1,6-bisphosphate aldolase from rabbit muscle Deposited 2007-08-06 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded PO4 PHOSPHATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.22 Å R-free 0.191
3B8D Fructose 1,6-bisphosphate aldolase from rabbit muscle Deposited 2007-11-01 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Mutation：E188Q Mutation：E188Q Mutation：E188Q Mutation：E188Q SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions SMALL TUBES；pH 7.4；293 K；40% ammonium sulphate 5mM EDTA, 100mM triethylamine, pH 7.4, SMALL TUBES, temperature 293K
Resolution 2.00 Å R-free 0.238
3BV4 Crystal structure of a rabbit muscle fructose-1,6-bisphosphate aldolase A dimer variant Deposited 2008-01-04 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 A 5–344（340 aa）
Mutation：D128V SO4 SULFATE ION × 12 13P 1,3-DIHYDROXYACETONEPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；291 K；0.2 M ammonium sulfate, 25% PEG 2K monomethyl ether, 100 mM sodium acetate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.70 Å R-free 0.215
3DFN D33N mutant fructose-1,6-bisphosphate aldolase from rabbit muscle Deposited 2008-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Mutation：D33N Mutation：D33N Mutation：D33N Mutation：D33N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.86 Å R-free 0.188
3DFP Phosphate ions in D33N mutant fructose-1,6-bisphosphate aldolase from rabbit muscle Deposited 2008-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Mutation：D33N Mutation：D33N Mutation：D33N Mutation：D33N PO4 PHOSPHATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.05 Å R-free 0.214
3DFQ D33S mutant fructose-1,6-bisphosphate aldolase from rabbit muscle Deposited 2008-06-12 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Mutation：D33S Mutation：D33S Mutation：D33S Mutation：D33S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.82 Å R-free 0.188
3DFS Dihydroxyacetone phosphate Schiff base intermediate in D33S mutant fructose-1,6-bisphosphate aldolase from rabbit muscle Deposited 2008-06-12 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Mutation：D33S Mutation：D33S Mutation：D33S Mutation：D33S 13P 1,3-DIHYDROXYACETONEPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.03 Å R-free 0.187
3DFT Phosphate ions in D33S mutant fructose-1,6-bisphosphate aldolase from rabbit muscle Deposited 2008-06-12 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Mutation：D33S Mutation：D33S Mutation：D33S Mutation：D33S PO4 PHOSPHATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.94 Å R-free 0.205
3LGE Crystal structure of rabbit muscle aldolase-SNX9 LC4 complex Deposited 2010-01-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG-MME 550, MgCl2, pH 7, Vapor Diffusion, Hanging drop, temperature 277K
Resolution 2.20 Å R-free 0.189
3TU9 Crystal structure of rabbit muscle aldolase bound with 5-O-methyl mannitol 1,6-phosphate Deposited 2011-09-16 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded 5MM 2-O-methyl-1,6-di-O-phosphono-D-mannitol × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；17.5% PEG4000, 0.1 M HEPES sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.09 Å R-free 0.201
5F4X Fructose-1,6-bisphosphate aldolase K229M mutant from rabbit muscle Deposited 2015-12-03 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Mutation：K229M Mutation：K229M Mutation：K229M Mutation：K229M GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；Sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.84 Å R-free 0.174
5TLE Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor 2-phosphate-naphthalene 6-bisphosphonate Deposited 2016-10-11 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded RD1 {[6-(phosphonooxy)naphthalen-2-yl]methylene}bis(phosphonic acid) × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；0.1M Sodium HEPES, 17.5% PEG 4000
Resolution 1.58 Å R-free 0.158
5TLH Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor 2-naphthol 6-bisphosphonate Deposited 2016-10-11 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded RD2 [(6-hydroxynaphthalen-2-yl)methylene]bis(phosphonic acid) × 4 MDN METHYLENEDIPHOSPHONIC ACID × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；0.1M Sodium HEPES, 17.5% PEG 4000
Resolution 2.20 Å R-free 0.188
5TLW Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor 1-phosphate-benzene 4-bisphosphonate Deposited 2016-10-12 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded RD3 {[4-(phosphonooxy)phenyl]methylene}bis(phosphonic acid) × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；0.1M Sodium HEPES, 17.5% PEG 4000
Resolution 2.29 Å R-free 0.191
5TLZ Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor naphthalene 2,6-bisphosphate Deposited 2016-10-12 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded N26 naphthalene-2,6-diyl bis[dihydrogen (phosphate)] × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；0.1M Sodium HEPES, 17.5% PEG 4000
Resolution 1.97 Å R-free 0.166
5VY5 Rabbit muscle aldolase using 200keV Deposited 2017-05-24 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample/grid was manually blotted for 4 seconds prior to immediate plunge-freezing in liquid nitrogen-cooled ethane.
Resolution 2.60 Å
6ALD RABBIT MUSCLE ALDOLASE A/FRUCTOSE-1,6-BISPHOSPHATE COMPLEX Deposited 1998-12-23 Different construct 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 1–363（363 aa）
Chain B 1–363（363 aa）
Chain C 1–363（363 aa）
Chain D 1–363（363 aa）
Mutation：K146A Mutation：K146A Mutation：K146A Mutation：K146A 2FP 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；pH 7.4
Resolution 2.30 Å R-free 0.274
6MWQ Single particle cryoEM structure of a DARPin-aldolase platform in complex with GFP Deposited 2018-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 16–348（333 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Grids were frozen on a manual plunger at the Scripps Research Institute Core Microscopy Facility in a 4 degrees C cold room humidified to >95%.
Resolution 3.00 Å
6MWQ Single particle cryoEM structure of a DARPin-aldolase platform in complex with GFP Deposited 2018-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 16–348（333 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Grids were frozen on a manual plunger at the Scripps Research Institute Core Microscopy Facility in a 4 degrees C cold room humidified to >95%.
Resolution 3.00 Å
6MWQ Single particle cryoEM structure of a DARPin-aldolase platform in complex with GFP Deposited 2018-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 16–348（333 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Grids were frozen on a manual plunger at the Scripps Research Institute Core Microscopy Facility in a 4 degrees C cold room humidified to >95%.
Resolution 3.00 Å
6MWQ Single particle cryoEM structure of a DARPin-aldolase platform in complex with GFP Deposited 2018-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 16–348（333 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Grids were frozen on a manual plunger at the Scripps Research Institute Core Microscopy Facility in a 4 degrees C cold room humidified to >95%.
Resolution 3.00 Å
6V20 Rabbit muscle aldolase determined using single-particle cryo-EM at 200 keV Deposited 2019-11-21 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 3–345（343 aa）
Chain B 3–345（343 aa）
Chain C 3–345（343 aa）
Chain D 3–345（343 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample/grid was manually blotted for 4 seconds prior to immediate plunge-freezing in liquid nitrogen-cooled ethane.
Resolution 2.13 Å
7K9L Aldolase, rabbit muscle (no beam-tilt refinement) Deposited 2020-09-29 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
7K9X Aldolase, rabbit muscle (beam-tilt refinement x1) Deposited 2020-09-29 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7KA2 Aldolase, rabbit muscle (beam-tilt refinement x2) Deposited 2020-09-29 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7KA3 Aldolase, rabbit muscle (beam-tilt refinement x3) Deposited 2020-09-29 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7KA4 Aldolase, rabbit muscle (beam-tilt refinement x4) Deposited 2020-09-29 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7VDC 3.28 A structure of the rabbit muscle aldolase Deposited 2021-09-06 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 1–364（364 aa）
Chain B 1–364（364 aa）
Chain C 1–364（364 aa）
Chain D 1–364（364 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
8EHG Rabbit muscle aldolase determined using single-particle cryo-EM with Apollo camera. Deposited 2022-09-14 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 1–364（364 aa）
Chain B 1–364（364 aa）
Chain C 1–364（364 aa）
Chain D 1–364（364 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；DTT are added freshly before use.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.24 Å
8EW2 Cryo-EM structure of Aldolase embedded in crystalline ice Deposited 2022-10-21 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 2–364（363 aa）
Chain B 2–364（363 aa）
Chain C 2–364（363 aa）
Chain D 2–364（363 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50-mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TWK Cryo-EM structure of Aldolase collected by EPU on Glacios at 2.6 Angstrom resolution Deposited 2023-08-21 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 2–345（344 aa）
Chain B 2–345（344 aa）
Chain C 2–345（344 aa）
Chain D 2–345（344 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8TWL Cryo-EM structure of Aldolase collected by SerialEM on Glacios at 2.7 Angstrom resolution Deposited 2023-08-21 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 2–345（344 aa）
Chain B 2–345（344 aa）
Chain C 2–345（344 aa）
Chain D 2–345（344 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8TWM Cryo-EM structure of Aldolase collected by Leginon on Glacios at 2.6 Angstrom resolution Deposited 2023-08-21 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 2–345（344 aa）
Chain B 2–345（344 aa）
Chain C 2–345（344 aa）
Chain D 2–345（344 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å

59 other PDB entries and 62 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ALDOA_RABIT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–363； UniProt 2–364 Author chain B； PDBConstruct 1–363； UniProt 2–364 Author chain C； PDBConstruct 1–363； UniProt 2–364 Author chain D； PDBConstruct 1–363； UniProt 2–364

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 3dfo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3dfo
Deposition date deposition_date2008-06-12
Structure title titleDihydroxyacetone phosphate Schiff base and enamine intermediates in D33N mutant fructose-1,6-bisphosphate aldolase from rabbit muscle
Keywords keywordsaldolase, mutant, iminium, Schiff base, enamine, intermediate, covalent, LYASE; LYASE
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_guinier35.17 Å
Radius of gyration Rg (electron density) rg_electron34.37 Å
Forward intensity I(0) i0365527000.00
Molecular weight molecular_weight153540.0 kDa
Excluded volume excluded_volume191870 ų
Envelope volume envelope_volume230190 ų
Hydration-shell volume shell_volume54932 ų
Envelope diameter envelope_diameter113.7 Å
Shell Rg shell_rg41.92 Å
Envelope Rg envelope_rg34.39 Å
Shape Rg shape_rg34.38 Å
Total Rg total_rg34.82 Å
Total atoms total_atoms10789
Residues n_residues1411
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 dmax112.0 Å
Rg (real space) rg_real35.03 Å
Rg uncertainty (real space) rg_real_error0.67 Å
I(0) (real space) i0_real3.6550e+08
I(0) uncertainty (real space) i0_real_error6.0770e+06
Rg (reciprocal space) rg_reciprocal35.12 Å
I(0) (reciprocal space) i0_reciprocal365600000.0000
Solution quality estimate total_estimate0.8969
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.3 Å
Skewness Skewness skewness0.183
Kurtosis Kurtosis kurtosis-0.494
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha69180000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.904
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3dfoa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.10 — Aldolase
Family Family familyc.1.10.1 — Class I aldolase
Domain ID domain_idd3dfob_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.10 — Aldolase
Family Family familyc.1.10.1 — Class I aldolase
Domain ID domain_idd3dfoc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.10 — Aldolase
Family Family familyc.1.10.1 — Class I aldolase
Domain ID domain_idd3dfod_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.10 — Aldolase
Family Family familyc.1.10.1 — Class I aldolase

CATH v4.4 (4 domains)

Domain ID domain_id3dfoA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id3dfoB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id3dfoC00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id3dfoD00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
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8. Citations (1)

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9. Files and Curves (10)