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6h9f

Structure of glutamate mutase reconstituted with bishomo-coenzyme B12

Method: X-RAY DIFFRACTION Dmax: 106.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate mutase sigma subunit

Clostridium cochlearium

UniProt P80078

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–137 Chain C； UniProt 1–137 Not recorded Glutamate mutase epsilon subunit × 2 （P80077） B12 COBALAMIN × 2 8ZB (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-propyl-oxolane-3,4-diol × 2 TAR D(-)-TARTARIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；6% (w/v) PEG-4000, 0.1 M DL-tartrate, pH=4.5, 2 mM CdCl2 Resolution 2.10 Å R-free 0.203

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 6H9F Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B1A GLUTAMATE MUTASE (B12-BINDING SUBUNIT), NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1998-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–137（137 aa） Fragment：B12-BINDING SUBUNIT
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；299 K；Ionic strength (raw mmCIF value) 10mM K2HPO4/KH2PO4；Pressure ATMOSPHERIC
NMR sample composition 10% H2O/90% D2O
Resolution not provided
1CB7 GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM RECONSTITUTED WITH METHYL-COBALAMIN Deposited 1999-03-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–137（137 aa）
Chain C 1–137（137 aa）
Not recorded COB CO-METHYLCOBALAMIN × 2 TAR D(-)-TARTARIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 2.00 Å R-free 0.218
1CCW STRUCTURE OF THE COENZYME B12 DEPENDENT ENZYME GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM Deposited 1999-03-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–137（137 aa） Fragment：B12-Binding Subunit
Chain C 1–137（137 aa） Fragment：B12-Binding Subunit
Not recorded CNC CYANOCOBALAMIN × 2 TAR D(-)-TARTARIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；pH 4.6, VAPOR DIFFUSION, HANGING DROP
Resolution 1.60 Å R-free 0.173
1I9C GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM: COMPLEX WITH ADENOSYLCOBALAMIN AND SUBSTRATE Deposited 2001-03-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–137（137 aa）
Chain C 1–137（137 aa）
Not recorded B12 COBALAMIN × 2 5AD 5'-DEOXYADENOSINE × 2 GLU GLUTAMIC ACID × 2 2AS (2S,3S)-3-methyl-aspartic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；PEG-4000, cadmium chloride, coenzyme B12, sodium glutamate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.90 Å R-free 0.221
6H9E Structure of glutamate mutase reconstituted with homo-coenzyme B12 Deposited 2018-08-03 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–137（137 aa）
Chain C 1–137（137 aa）
Not recorded B12 COBALAMIN × 2 FWK (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol × 2 TAR D(-)-TARTARIC ACID × 2 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；6% (w/v) PEG-4000, 0.1 M DL-tartrate, pH=4.5, 2 mM CdCl2
Resolution 1.82 Å R-free 0.168

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GMSS_CLOCO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–137； UniProt 1–137 Author chain C； PDBConstruct 1–137； UniProt 1–137

Glutamate mutase epsilon subunit

Clostridium cochlearium

UniProt P80077

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 1–483 Chain D； UniProt 1–483 Not recorded Glutamate mutase sigma subunit × 2 （P80078） B12 COBALAMIN × 2 8ZB (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-propyl-oxolane-3,4-diol × 2 TAR D(-)-TARTARIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；6% (w/v) PEG-4000, 0.1 M DL-tartrate, pH=4.5, 2 mM CdCl2 Resolution 2.10 Å R-free 0.203

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 6H9F Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CB7 GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM RECONSTITUTED WITH METHYL-COBALAMIN Deposited 1999-03-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–483（483 aa）
Chain D 1–483（483 aa）
Not recorded COB CO-METHYLCOBALAMIN × 2 TAR D(-)-TARTARIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 2.00 Å R-free 0.218
1CCW STRUCTURE OF THE COENZYME B12 DEPENDENT ENZYME GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM Deposited 1999-03-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–483（483 aa） Fragment：E chain
Chain D 1–483（483 aa） Fragment：E chain
Not recorded CNC CYANOCOBALAMIN × 2 TAR D(-)-TARTARIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；pH 4.6, VAPOR DIFFUSION, HANGING DROP
Resolution 1.60 Å R-free 0.173
1I9C GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM: COMPLEX WITH ADENOSYLCOBALAMIN AND SUBSTRATE Deposited 2001-03-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–483（483 aa）
Chain D 1–483（483 aa）
Not recorded B12 COBALAMIN × 2 5AD 5'-DEOXYADENOSINE × 2 GLU GLUTAMIC ACID × 2 2AS (2S,3S)-3-methyl-aspartic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；PEG-4000, cadmium chloride, coenzyme B12, sodium glutamate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.90 Å R-free 0.221
6H9E Structure of glutamate mutase reconstituted with homo-coenzyme B12 Deposited 2018-08-03 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–483（483 aa）
Chain D 1–483（483 aa）
Not recorded B12 COBALAMIN × 2 FWK (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol × 2 TAR D(-)-TARTARIC ACID × 2 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；6% (w/v) PEG-4000, 0.1 M DL-tartrate, pH=4.5, 2 mM CdCl2
Resolution 1.82 Å R-free 0.168

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GLME_CLOCO
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–483； UniProt 1–483 Author chain D； PDBConstruct 1–483； UniProt 1–483

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 6h9f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6h9f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6h9f
Deposition date deposition_date2018-08-03
Structure title titleStructure of glutamate mutase reconstituted with bishomo-coenzyme B12
Keywords keywordsCOENZYME B12, CO-C-BOND, RADICAL REACTION, TIM-BARREL, ROSSMAN-FOLD, ISOMERASE; ISOMERASE
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_guinier33.70 Å
Radius of gyration Rg (electron density) rg_electron33.11 Å
Forward intensity I(0) i0298125000.00
Molecular weight molecular_weight140220.0 kDa
Excluded volume excluded_volume175800 ų
Envelope volume envelope_volume203460 ų
Hydration-shell volume shell_volume49596 ų
Envelope diameter envelope_diameter110.3 Å
Shell Rg shell_rg41.07 Å
Envelope Rg envelope_rg33.37 Å
Shape Rg shape_rg33.11 Å
Total Rg total_rg33.63 Å
Total atoms total_atoms9846
Residues n_residues1240
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 dmax106.3 Å
Rg (real space) rg_real33.65 Å
Rg uncertainty (real space) rg_real_error0.80 Å
I(0) (real space) i0_real2.9810e+08
I(0) uncertainty (real space) i0_real_error4.7080e+06
Rg (reciprocal space) rg_reciprocal33.68 Å
I(0) (reciprocal space) i0_reciprocal298100000.0000
Solution quality estimate total_estimate0.9015
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.5 Å
Skewness Skewness skewness0.268
Kurtosis Kurtosis kurtosis-0.552
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha156300000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.913
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6h9fa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.6 — Cobalamin (vitamin B12)-binding domain
Family Family familyc.23.6.1 — Cobalamin (vitamin B12)-binding domain
Domain ID domain_idd6h9fb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.19 — Cobalamin (vitamin B12)-dependent enzymes
Family Family familyc.1.19.2 — Glutamate mutase, large subunit
Domain ID domain_idd6h9fc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.6 — Cobalamin (vitamin B12)-binding domain
Family Family familyc.23.6.1 — Cobalamin (vitamin B12)-binding domain
Domain ID domain_idd6h9fd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.19 — Cobalamin (vitamin B12)-dependent enzymes
Family Family familyc.1.19.2 — Glutamate mutase, large subunit

CATH v4.4 (6 domains)

Domain ID domain_id6h9fA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily280 — Cobalamin-binding domain
Domain ID domain_id6h9fB01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily240 — Methylmalonyl-CoA mutase
Domain ID domain_id6h9fB02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology970 — Glutamate mutase, C-terminal domain
Homologous superfamily homologous superfamily10 —
Domain ID domain_id6h9fC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily280 — Cobalamin-binding domain
Domain ID domain_id6h9fD01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily240 — Methylmalonyl-CoA mutase
Domain ID domain_id6h9fD02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology970 — Glutamate mutase, C-terminal domain
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)