SAXSdb — 1dio

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (DIOL DEHYDRATASE)

Klebsiella oxytoca

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–554 Chain L； UniProt 1–554	Not recorded	PROTEIN (DIOL DEHYDRATASE) × 2 （Q59471） PROTEIN (DIOL DEHYDRATASE) × 2 （Q59472） K POTASSIUM ION × 2 PGO S-1,2-PROPANEDIOL × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；pH 8.0	Resolution 2.20 Å R-free 0.236

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 1DIO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EEX CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA Deposited 2000-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Fragment：ALPHA CHAIN Chain L 1–554（554 aa） Fragment：ALPHA CHAIN	Not recorded	K POTASSIUM ION × 4 COY CO-(ADENIN-9-YL-PENTYL)-COBALAMIN × 2 PGO S-1,2-PROPANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion, sandwich drop；pH 8；277 K；PEG 6000, potassium phospate, Tris-HCl, LDAO, ammonium sulfate, propane diol, adeninylpentylcobalamin,, pH 8.0, vapor diffusion, sandwich drop, temperature 277K	Resolution 1.70 Å R-free 0.226
1EGM CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K. Deposited 2000-02-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Fragment：ALPHA CHAIN Chain L 1–554（554 aa） Fragment：ALPHA CHAIN	Not recorded	K POTASSIUM ION × 2 CNC CYANOCOBALAMIN × 2 PGO S-1,2-PROPANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SANDWICH；pH 8；277 K；PEG6000, potassium phosphate, Tris, lauryldimethylamine oxide, ammonium sulfate, propane diol, cyanocobalamin, pH 8.0, VAPOR DIFFUSION, SANDWICH, temperature 277K	Resolution 1.85 Å R-free 0.249
1EGV CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSELLA OXYTOCA UNDER THE ILLUMINATED CONDITION. Deposited 2000-02-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Fragment：ALPHA CHAIN Chain L 1–554（554 aa） Fragment：ALPHA CHAIN	Not recorded	K POTASSIUM ION × 4 COY CO-(ADENIN-9-YL-PENTYL)-COBALAMIN × 2 PGO S-1,2-PROPANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION sandwich drop；pH 8；277 K；PEG 6000, potassium phospate, Tris-HCl, LDAO, ammonium sulfate, propane diol, adeninlpentylcobalamin,, pH 8.0, VAPOR DIFFUSION sandwich drop, temperature 277K	Resolution 1.75 Å R-free 0.214
1IWB Crystal structure of diol dehydratase Deposited 2002-05-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Chain L 1–554（554 aa）	Not recorded	K POTASSIUM ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；278 K；PEG6000, potassium phosphate, Tris, lithium chloride, N,N-dimethyllaurylamineoxide, pH 8.0, VAPOR DIFFUSION, temperature 278K	Resolution 1.85 Å R-free 0.256
1IWB Crystal structure of diol dehydratase Deposited 2002-05-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Chain L 1–554（554 aa）	Not recorded	K POTASSIUM ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；278 K；PEG6000, potassium phosphate, Tris, lithium chloride, N,N-dimethyllaurylamineoxide, pH 8.0, VAPOR DIFFUSION, temperature 278K	Resolution 1.85 Å R-free 0.256
1UC4 Structure of diol dehydratase complexed with (S)-1,2-propanediol Deposited 2003-04-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Chain L 1–554（554 aa）	Not recorded	NH4 AMMONIUM ION × 4 K POTASSIUM ION × 2 PGO S-1,2-PROPANEDIOL × 2 CNC CYANOCOBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；278 K；PEG6000, ammonium sulfate, Tris, (S)-1,2,-propanediol, pH 8.0, VAPOR DIFFUSION, temperature 278K	Resolution 1.80 Å R-free 0.230
1UC5 Structure of diol dehydratase complexed with (R)-1,2-propanediol Deposited 2003-04-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Chain L 1–554（554 aa）	Not recorded	K POTASSIUM ION × 2 NH4 AMMONIUM ION × 4 PGR R-1,2-PROPANEDIOL × 2 CNC CYANOCOBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；278 K；PEG6000, ammonium sulfate, Tris, (R)-1,2,-propanediol, pH 8.0, VAPOR DIFFUSION, temperature 278K	Resolution 2.30 Å R-free 0.255
3AUJ Structure of diol dehydratase complexed with glycerol Deposited 2011-02-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Chain L 1–554（554 aa）	Not recorded	GOL GLYCEROL × 2 CA CALCIUM ION × 2 PO4 PHOSPHATE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；14-18%(W/V) PEG 6000, 0.23-0.25M AMMONIUM SULFATE, 0.02M TRIS-HCL, 0.2%(W/V) LDAO, pH 8.0, VAPOR DIFFUSION, temperature 277K	Resolution 2.10 Å R-free 0.191
5YRT Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal Deposited 2017-11-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Chain D 1–554（554 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 5AD 5'-DEOXYADENOSINE × 2 CL CHLORIDE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.70 Å R-free 0.187
5YRT Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal Deposited 2017-11-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–554（554 aa） Chain J 1–554（554 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 5AD 5'-DEOXYADENOSINE × 2 CL CHLORIDE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.70 Å R-free 0.187
5YRV Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal Deposited 2017-11-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Chain D 1–554（554 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 PGO S-1,2-PROPANEDIOL × 2 5AD 5'-DEOXYADENOSINE × 2 CL CHLORIDE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.55 Å R-free 0.181
5YRV Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal Deposited 2017-11-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–554（554 aa） Chain J 1–554（554 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 PGO S-1,2-PROPANEDIOL × 1 5AD 5'-DEOXYADENOSINE × 2 CL CHLORIDE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.55 Å R-free 0.181
5YSH Diol dehydratase - alpha/T172A mutant complexed with AdoCbl, aerobically-prepared crystal Deposited 2017-11-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Chain D 1–554（554 aa）	Mutation：T172A Mutation：T172A	CA CALCIUM ION × 2 K POTASSIUM ION × 4 PGO S-1,2-PROPANEDIOL × 2 5AD 5'-DEOXYADENOSINE × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.90 Å R-free 0.191
5YSH Diol dehydratase - alpha/T172A mutant complexed with AdoCbl, aerobically-prepared crystal Deposited 2017-11-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–554（554 aa） Chain J 1–554（554 aa）	Mutation：T172A Mutation：T172A	CA CALCIUM ION × 2 K POTASSIUM ION × 4 PGO S-1,2-PROPANEDIOL × 2 5AD 5'-DEOXYADENOSINE × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.90 Å R-free 0.191
7XRK Diol dehydratase complexed with AdoMeCbl Deposited 2022-05-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Chain D 1–554（554 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 2 FWK (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；25% (w/v) PEG6000, 50 mM HEPES pH 8.0, 0.2 M ammonium sulfate	Resolution 2.30 Å R-free 0.225
7XRL Diol dehydratase complexed with AdoMeCbl and 1,2-propanediol Deposited 2022-05-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Chain D 1–554（554 aa）	Not recorded	PGO S-1,2-PROPANEDIOL × 2 CA CALCIUM ION × 2 K POTASSIUM ION × 2 NH4 AMMONIUM ION × 2 FWK (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；25% (w/v) PEG6000, 50 mM HEPES pH 8.0, 0.2 M ammonium sulfate	Resolution 1.75 Å R-free 0.206

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

View Construct and Data Evidence

UniProt name	Q59470_KLEOX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–554； UniProt 1–554 Author chain L； PDBConstruct 1–554； UniProt 1–554

PROTEIN (DIOL DEHYDRATASE)

Klebsiella oxytoca

UniProt Q59471

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain B； UniProt 1–224 Chain E； UniProt 1–224	Not recorded	PROTEIN (DIOL DEHYDRATASE) × 2 （Q59470） PROTEIN (DIOL DEHYDRATASE) × 2 （Q59472） K POTASSIUM ION × 2 PGO S-1,2-PROPANEDIOL × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；pH 8.0	Resolution 2.20 Å R-free 0.236

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 1DIO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EEX CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA Deposited 2000-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–224（224 aa） Fragment：BETA CHAIN Chain E 1–224（224 aa） Fragment：BETA CHAIN	Not recorded	K POTASSIUM ION × 4 COY CO-(ADENIN-9-YL-PENTYL)-COBALAMIN × 2 PGO S-1,2-PROPANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion, sandwich drop；pH 8；277 K；PEG 6000, potassium phospate, Tris-HCl, LDAO, ammonium sulfate, propane diol, adeninylpentylcobalamin,, pH 8.0, vapor diffusion, sandwich drop, temperature 277K	Resolution 1.70 Å R-free 0.226
1EGM CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K. Deposited 2000-02-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–224（224 aa） Fragment：BETA CHAIN Chain E 1–224（224 aa） Fragment：BETA CHAIN	Not recorded	K POTASSIUM ION × 2 CNC CYANOCOBALAMIN × 2 PGO S-1,2-PROPANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SANDWICH；pH 8；277 K；PEG6000, potassium phosphate, Tris, lauryldimethylamine oxide, ammonium sulfate, propane diol, cyanocobalamin, pH 8.0, VAPOR DIFFUSION, SANDWICH, temperature 277K	Resolution 1.85 Å R-free 0.249
1EGV CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSELLA OXYTOCA UNDER THE ILLUMINATED CONDITION. Deposited 2000-02-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–224（224 aa） Fragment：BETA CHAIN Chain E 1–224（224 aa） Fragment：BETA CHAIN	Not recorded	K POTASSIUM ION × 4 COY CO-(ADENIN-9-YL-PENTYL)-COBALAMIN × 2 PGO S-1,2-PROPANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION sandwich drop；pH 8；277 K；PEG 6000, potassium phospate, Tris-HCl, LDAO, ammonium sulfate, propane diol, adeninlpentylcobalamin,, pH 8.0, VAPOR DIFFUSION sandwich drop, temperature 277K	Resolution 1.75 Å R-free 0.214
1IWB Crystal structure of diol dehydratase Deposited 2002-05-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–224（224 aa） Chain E 1–224（224 aa）	Not recorded	K POTASSIUM ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；278 K；PEG6000, potassium phosphate, Tris, lithium chloride, N,N-dimethyllaurylamineoxide, pH 8.0, VAPOR DIFFUSION, temperature 278K	Resolution 1.85 Å R-free 0.256
1IWB Crystal structure of diol dehydratase Deposited 2002-05-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–224（224 aa） Chain E 1–224（224 aa）	Not recorded	K POTASSIUM ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；278 K；PEG6000, potassium phosphate, Tris, lithium chloride, N,N-dimethyllaurylamineoxide, pH 8.0, VAPOR DIFFUSION, temperature 278K	Resolution 1.85 Å R-free 0.256
1UC4 Structure of diol dehydratase complexed with (S)-1,2-propanediol Deposited 2003-04-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–224（224 aa） Chain E 1–224（224 aa）	Not recorded	NH4 AMMONIUM ION × 4 K POTASSIUM ION × 2 PGO S-1,2-PROPANEDIOL × 2 CNC CYANOCOBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；278 K；PEG6000, ammonium sulfate, Tris, (S)-1,2,-propanediol, pH 8.0, VAPOR DIFFUSION, temperature 278K	Resolution 1.80 Å R-free 0.230
1UC5 Structure of diol dehydratase complexed with (R)-1,2-propanediol Deposited 2003-04-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–224（224 aa） Chain E 1–224（224 aa）	Not recorded	K POTASSIUM ION × 2 NH4 AMMONIUM ION × 4 PGR R-1,2-PROPANEDIOL × 2 CNC CYANOCOBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；278 K；PEG6000, ammonium sulfate, Tris, (R)-1,2,-propanediol, pH 8.0, VAPOR DIFFUSION, temperature 278K	Resolution 2.30 Å R-free 0.255
3AUJ Structure of diol dehydratase complexed with glycerol Deposited 2011-02-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–224（224 aa） Chain E 1–224（224 aa）	Not recorded	GOL GLYCEROL × 2 CA CALCIUM ION × 2 PO4 PHOSPHATE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；14-18%(W/V) PEG 6000, 0.23-0.25M AMMONIUM SULFATE, 0.02M TRIS-HCL, 0.2%(W/V) LDAO, pH 8.0, VAPOR DIFFUSION, temperature 277K	Resolution 2.10 Å R-free 0.191
5YRT Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal Deposited 2017-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 46–224（179 aa） Chain E 46–224（179 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 5AD 5'-DEOXYADENOSINE × 2 CL CHLORIDE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.70 Å R-free 0.187
5YRT Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal Deposited 2017-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 46–224（179 aa） Chain K 46–224（179 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 5AD 5'-DEOXYADENOSINE × 2 CL CHLORIDE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.70 Å R-free 0.187
5YRV Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal Deposited 2017-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 46–224（179 aa） Chain E 46–224（179 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 PGO S-1,2-PROPANEDIOL × 2 5AD 5'-DEOXYADENOSINE × 2 CL CHLORIDE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.55 Å R-free 0.181
5YRV Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal Deposited 2017-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 46–224（179 aa） Chain K 46–224（179 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 PGO S-1,2-PROPANEDIOL × 1 5AD 5'-DEOXYADENOSINE × 2 CL CHLORIDE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.55 Å R-free 0.181
5YSH Diol dehydratase - alpha/T172A mutant complexed with AdoCbl, aerobically-prepared crystal Deposited 2017-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 46–224（179 aa） Chain E 46–224（179 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 PGO S-1,2-PROPANEDIOL × 2 5AD 5'-DEOXYADENOSINE × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.90 Å R-free 0.191
5YSH Diol dehydratase - alpha/T172A mutant complexed with AdoCbl, aerobically-prepared crystal Deposited 2017-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 46–224（179 aa） Chain K 46–224（179 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 PGO S-1,2-PROPANEDIOL × 2 5AD 5'-DEOXYADENOSINE × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.90 Å R-free 0.191
7XRK Diol dehydratase complexed with AdoMeCbl Deposited 2022-05-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 46–224（179 aa） Chain E 46–224（179 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 2 FWK (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；25% (w/v) PEG6000, 50 mM HEPES pH 8.0, 0.2 M ammonium sulfate	Resolution 2.30 Å R-free 0.225
7XRL Diol dehydratase complexed with AdoMeCbl and 1,2-propanediol Deposited 2022-05-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 46–224（179 aa） Chain E 46–224（179 aa）	Not recorded	PGO S-1,2-PROPANEDIOL × 2 CA CALCIUM ION × 2 K POTASSIUM ION × 2 NH4 AMMONIUM ION × 2 FWK (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；25% (w/v) PEG6000, 50 mM HEPES pH 8.0, 0.2 M ammonium sulfate	Resolution 1.75 Å R-free 0.206

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

View Construct and Data Evidence

UniProt name	Q59471_KLEOX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–224； UniProt 1–224 Author chain E； PDBConstruct 1–224； UniProt 1–224

PROTEIN (DIOL DEHYDRATASE)

Klebsiella oxytoca

UniProt Q59472

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain G； UniProt 1–173 Chain M； UniProt 1–173	Not recorded	PROTEIN (DIOL DEHYDRATASE) × 2 （Q59470） PROTEIN (DIOL DEHYDRATASE) × 2 （Q59471） K POTASSIUM ION × 2 PGO S-1,2-PROPANEDIOL × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；pH 8.0	Resolution 2.20 Å R-free 0.236

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 1DIO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EEX CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA Deposited 2000-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–173（173 aa） Fragment：GAMMA CHAIN Chain M 1–173（173 aa） Fragment：GAMMA CHAIN	Not recorded	K POTASSIUM ION × 4 COY CO-(ADENIN-9-YL-PENTYL)-COBALAMIN × 2 PGO S-1,2-PROPANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion, sandwich drop；pH 8；277 K；PEG 6000, potassium phospate, Tris-HCl, LDAO, ammonium sulfate, propane diol, adeninylpentylcobalamin,, pH 8.0, vapor diffusion, sandwich drop, temperature 277K	Resolution 1.70 Å R-free 0.226
1EGM CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K. Deposited 2000-02-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–173（173 aa） Fragment：GAMMA CHAIN Chain M 1–173（173 aa） Fragment：GAMMA CHAIN	Not recorded	K POTASSIUM ION × 2 CNC CYANOCOBALAMIN × 2 PGO S-1,2-PROPANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SANDWICH；pH 8；277 K；PEG6000, potassium phosphate, Tris, lauryldimethylamine oxide, ammonium sulfate, propane diol, cyanocobalamin, pH 8.0, VAPOR DIFFUSION, SANDWICH, temperature 277K	Resolution 1.85 Å R-free 0.249
1EGV CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSELLA OXYTOCA UNDER THE ILLUMINATED CONDITION. Deposited 2000-02-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–173（173 aa） Fragment：GAMMA CHAIN Chain M 1–173（173 aa） Fragment：GAMMA CHAIN	Not recorded	K POTASSIUM ION × 4 COY CO-(ADENIN-9-YL-PENTYL)-COBALAMIN × 2 PGO S-1,2-PROPANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION sandwich drop；pH 8；277 K；PEG 6000, potassium phospate, Tris-HCl, LDAO, ammonium sulfate, propane diol, adeninlpentylcobalamin,, pH 8.0, VAPOR DIFFUSION sandwich drop, temperature 277K	Resolution 1.75 Å R-free 0.214
1IWB Crystal structure of diol dehydratase Deposited 2002-05-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–173（173 aa） Chain M 1–173（173 aa）	Not recorded	K POTASSIUM ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；278 K；PEG6000, potassium phosphate, Tris, lithium chloride, N,N-dimethyllaurylamineoxide, pH 8.0, VAPOR DIFFUSION, temperature 278K	Resolution 1.85 Å R-free 0.256
1IWB Crystal structure of diol dehydratase Deposited 2002-05-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–173（173 aa） Chain M 1–173（173 aa）	Not recorded	K POTASSIUM ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；278 K；PEG6000, potassium phosphate, Tris, lithium chloride, N,N-dimethyllaurylamineoxide, pH 8.0, VAPOR DIFFUSION, temperature 278K	Resolution 1.85 Å R-free 0.256
1UC4 Structure of diol dehydratase complexed with (S)-1,2-propanediol Deposited 2003-04-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–173（173 aa） Chain M 1–173（173 aa）	Not recorded	NH4 AMMONIUM ION × 4 K POTASSIUM ION × 2 PGO S-1,2-PROPANEDIOL × 2 CNC CYANOCOBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；278 K；PEG6000, ammonium sulfate, Tris, (S)-1,2,-propanediol, pH 8.0, VAPOR DIFFUSION, temperature 278K	Resolution 1.80 Å R-free 0.230
1UC5 Structure of diol dehydratase complexed with (R)-1,2-propanediol Deposited 2003-04-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–173（173 aa） Chain M 1–173（173 aa）	Not recorded	K POTASSIUM ION × 2 NH4 AMMONIUM ION × 4 PGR R-1,2-PROPANEDIOL × 2 CNC CYANOCOBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；278 K；PEG6000, ammonium sulfate, Tris, (R)-1,2,-propanediol, pH 8.0, VAPOR DIFFUSION, temperature 278K	Resolution 2.30 Å R-free 0.255
3AUJ Structure of diol dehydratase complexed with glycerol Deposited 2011-02-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–173（173 aa） Chain M 1–173（173 aa）	Not recorded	GOL GLYCEROL × 2 CA CALCIUM ION × 2 PO4 PHOSPHATE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；14-18%(W/V) PEG 6000, 0.23-0.25M AMMONIUM SULFATE, 0.02M TRIS-HCL, 0.2%(W/V) LDAO, pH 8.0, VAPOR DIFFUSION, temperature 277K	Resolution 2.10 Å R-free 0.191
5YRT Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal Deposited 2017-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 38–173（136 aa） Chain F 38–173（136 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 5AD 5'-DEOXYADENOSINE × 2 CL CHLORIDE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.70 Å R-free 0.187
5YRT Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal Deposited 2017-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 38–173（136 aa） Chain L 38–173（136 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 5AD 5'-DEOXYADENOSINE × 2 CL CHLORIDE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.70 Å R-free 0.187
5YRV Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal Deposited 2017-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 38–173（136 aa） Chain F 38–173（136 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 PGO S-1,2-PROPANEDIOL × 2 5AD 5'-DEOXYADENOSINE × 2 CL CHLORIDE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.55 Å R-free 0.181
5YRV Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal Deposited 2017-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 38–173（136 aa） Chain L 38–173（136 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 PGO S-1,2-PROPANEDIOL × 1 5AD 5'-DEOXYADENOSINE × 2 CL CHLORIDE ION × 6 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.55 Å R-free 0.181
5YSH Diol dehydratase - alpha/T172A mutant complexed with AdoCbl, aerobically-prepared crystal Deposited 2017-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 38–173（136 aa） Chain F 38–173（136 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 PGO S-1,2-PROPANEDIOL × 2 5AD 5'-DEOXYADENOSINE × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.90 Å R-free 0.191
5YSH Diol dehydratase - alpha/T172A mutant complexed with AdoCbl, aerobically-prepared crystal Deposited 2017-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 38–173（136 aa） Chain L 38–173（136 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 4 PGO S-1,2-PROPANEDIOL × 2 5AD 5'-DEOXYADENOSINE × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6	Resolution 1.90 Å R-free 0.191
7XRK Diol dehydratase complexed with AdoMeCbl Deposited 2022-05-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 38–173（136 aa） Chain F 38–173（136 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 2 FWK (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；25% (w/v) PEG6000, 50 mM HEPES pH 8.0, 0.2 M ammonium sulfate	Resolution 2.30 Å R-free 0.225
7XRL Diol dehydratase complexed with AdoMeCbl and 1,2-propanediol Deposited 2022-05-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 38–173（136 aa） Chain F 38–173（136 aa）	Not recorded	PGO S-1,2-PROPANEDIOL × 2 CA CALCIUM ION × 2 K POTASSIUM ION × 2 NH4 AMMONIUM ION × 2 FWK (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol × 2 B12 COBALAMIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；25% (w/v) PEG6000, 50 mM HEPES pH 8.0, 0.2 M ammonium sulfate	Resolution 1.75 Å R-free 0.206

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

View Construct and Data Evidence

UniProt name	Q59472_KLEOX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–173； UniProt 1–173 Author chain M； PDBConstruct 1–173； UniProt 1–173

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dio
Deposition date deposition_date	1999-01-27
Structure title title	DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA
Keywords keywords	COENZYME B12, PROPANEDIOL, POTASSIUM ION, TIM BARREL, LYASE; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	37.42 Å
Radius of gyration Rg (electron density) rg_electron	37.17 Å
Forward intensity I(0) i0	565415000.00
Molecular weight molecular_weight	192680.0 kDa
Excluded volume excluded_volume	240340 Å³
Envelope volume envelope_volume	278610 Å³
Hydration-shell volume shell_volume	60581 Å³
Envelope diameter envelope_diameter	125.5 Å
Shell Rg shell_rg	44.81 Å
Envelope Rg envelope_rg	37.51 Å
Shape Rg shape_rg	37.18 Å
Total Rg total_rg	37.50 Å
Total atoms total_atoms	13516
Residues n_residues	1734
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	123.6 Å
Rg (real space) rg_real	37.45 Å
Rg uncertainty (real space) rg_real_error	0.89 Å
I(0) (real space) i0_real	5.6540e+08
I(0) uncertainty (real space) i0_real_error	8.8330e+06
Rg (reciprocal space) rg_reciprocal	37.44 Å
I(0) (reciprocal space) i0_reciprocal	565400000.0000
Solution quality estimate total_estimate	0.8810
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.2 Å
Skewness Skewness skewness	0.377
Kurtosis Kurtosis kurtosis	-0.451
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	168700000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.920

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	PROTEIN (DIOL DEHYDRATASE)
Molecular weight formula_weight	60408.1 kDa
EC 编号 ec_number	4.2.1.28
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,L
Atom count atom_count	13912

MRSKRFEALAKRPVNQDGFVKEWIEEGFIAMESPNDPKPSIKIVNGAVTELDGKPVSDFDLIDHFIARYGINLNRAEEVMAMDSVKLANMLCDPNVKRSEIVPLTTAMTPAKIVEVVSHMNVVEMMMAMQKMRARRTPSQQAHVTNVKDNPVQIAADAAEGAWRGFDEQETTVAVARYAPFNAIALLVGSQVGRPGVLTQCSLEEATELKLGMLGHTCYAETISVYGTEPVFTDGDDTPWSKGFLASSYASRGLKMRFTSGSGSEVQMGYAEGKSMLYLEARCIYITKAAGVQGLQNGSVSCIGVPSAVPSGIRAVLAENLICSSLDLECASSNDQTFTHSDMRRTARLLMQFLPGTDFISSGYSAVPNYDNMFAGSNEDAEDFDDYNVIQRDLKVDGGLRPVREEDVIAIRNKAARALQAVFAGMGLPPITDEEVEAATYAHGSKDMPERNIVEDIKFAQEIINKNRNGLEVVKALAQGGFTDVAQDMLNIQKAKLTGDYLHTSAIIVGDGQVLSAVNDVNDYAGPATGYRLQGERWEEIKNIPGALDPNEID

来源 Source

来源生物 organism	Klebsiella oxytoca
NCBI Class编号 ncbi_taxonomy_id	571
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PROTEIN (DIOL DEHYDRATASE)
Molecular weight formula_weight	24141.7 kDa
EC 编号 ec_number	4.2.1.28
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MEINEKLLRQIIEDVLSEMKGSDKPVSFNAPAASAAPQATPPAGDGFLTEVGEARQGTQQDEVIIAVGPAFGLAQTVNIVGIPHKSILREVIAGIEEEGIKARVIRCFKSSDVAFVAVEGNRLSGSGISIGIQSKGTTVIHQQGLPPLSNLELFPQAPLLTLETYRQIGKNAARYAKRESPQPVPTLNDQMARPKYQAKSAILHIKETKYVVTGKNPQELRVAL

来源 Source

来源生物 organism	Klebsiella oxytoca
NCBI Class编号 ncbi_taxonomy_id	571
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	PROTEIN (DIOL DEHYDRATASE)
Molecular weight formula_weight	19198.7 kDa
EC 编号 ec_number	4.2.1.28
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,M

MNTDAIESMVRDVLSRMNSLQGEAPAAAPAAGGASRSARVSDYPLANKHPEWVKTATNKTLDDFTLENVLSNKVTAQDMRITPETLRLQASIAKDAGRDRLAMNFERAAELTAVPDDRILEIYNALRPYRSTKEELLAIADDLESRYQAKICAAFVREAATLYVERKKLKGDD

来源 Source

来源生物 organism	Klebsiella oxytoca
NCBI Class编号 ncbi_taxonomy_id	571
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	S-1,2-PROPANEDIOL
Molecular weight formula_weight	76.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	COBALAMIN
Molecular weight formula_weight	1330.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	396

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1dioa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
Family Family family	c.1.19.3 — Diol dehydratase, alpha subunit

Domain ID domain_id	d1diob_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.3 — B12-dependent dehydatase associated subunit
Family Family family	c.51.3.1 — Diol dehydratase, beta subunit

Domain ID domain_id	d1dioe_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.3 — B12-dependent dehydatase associated subunit
Family Family family	c.51.3.1 — Diol dehydratase, beta subunit

Domain ID domain_id	d1diog_
Class class	a — All alpha proteins
Fold Fold fold	a.23 — Open three-helical up-and-down bundle
Superfamily Superfamily superfamily	a.23.2 — Diol dehydratase, gamma subunit
Family Family family	a.23.2.1 — Diol dehydratase, gamma subunit

Domain ID domain_id	d1diol_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
Family Family family	c.1.19.3 — Diol dehydratase, alpha subunit

Domain ID domain_id	d1diom_
Class class	a — All alpha proteins
Fold Fold fold	a.23 — Open three-helical up-and-down bundle
Superfamily Superfamily superfamily	a.23.2 — Diol dehydratase, gamma subunit
Family Family family	a.23.2.1 — Diol dehydratase, gamma subunit

CATH v4.4 (6 domains)

Domain ID domain_id	1dioA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	350 — Diol/glycerol dehydratase, large subunit

Domain ID domain_id	1dioB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10150 — B12-dependent dehydatase associated subunit

Domain ID domain_id	1dioE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10150 — B12-dependent dehydatase associated subunit

Domain ID domain_id	1dioG02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1510 — Hypothetical Protein Yqey; Chain: A; domain1
Homologous superfamily homologous superfamily	20 — Propanediol/glycerol dehydratase, small subunit

Domain ID domain_id	1dioL00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	350 — Diol/glycerol dehydratase, large subunit

Domain ID domain_id	1dioM02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1510 — Hypothetical Protein Yqey; Chain: A; domain1
Homologous superfamily homologous superfamily	20 — Propanediol/glycerol dehydratase, small subunit

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8. Citations (1)

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Unit-cell length a length_a	76.200 Å
Unit-cell length b length_b	122.300 Å
Unit-cell length c length_c	209.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1880
R_work r_work	0.1870
R_free r_free	0.2360

fit	/app/data/saxs_computation/di/1dio/1dio.fit
pddf	/app/data/pr_computation/di/1dio/1dio.pr.out
profile	/app/data/saxs_computation/di/1dio/1dio.dat

DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (DIOL DEHYDRATASE)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (DIOL DEHYDRATASE)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (DIOL DEHYDRATASE)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)