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6bdy

Crystal Structure of the MetH Reactivation Domain bound to Sinefungin

Method: X-RAY DIFFRACTION Dmax: 68.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Methionine synthase

Escherichia coli

UniProt P13009

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 897–1227 Fragment：reactivation domain SFG SINEFUNGIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；28% PEG 6000, 100mM Tris pH 7.3, 300mM magnesium acetate:15mg/mL protein, 3mM sinefungin, 10mM Tris 7.2, 10mM EDTA, 2:2uL Resolution 1.51 Å R-free 0.186

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 6BDY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BMT HOW A PROTEIN BINDS B12: A 3.O ANGSTROM X-RAY STRUCTURE OF THE B12-BINDING DOMAINS OF METHIONINE SYNTHASE Deposited 1994-09-02 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 650–895（246 aa）
Chain B 650–895（246 aa）
Not recorded COB CO-METHYLCOBALAMIN × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1K7Y E. coli MetH C-terminal fragment (649-1227) Deposited 2001-10-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 651–1227（577 aa） Fragment：c-terminal activation complex, residues 651-1227
Mutation：H759G SO4 SULFATE ION × 10 B12 COBALAMIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；cacodylate, ammonium sulfate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.00 Å R-free 0.276
1K98 AdoMet complex of MetH C-terminal fragment Deposited 2001-10-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 651–1227（577 aa） Fragment：c-terminal activation complex, residues 651-1227
Mutation：H759G SO4 SULFATE ION × 1 B12 COBALAMIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；cacodylate, ammonium sulfate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.75 Å R-free 0.363
1MSK METHIONINE SYNTHASE (ACTIVATION DOMAIN) Deposited 1996-08-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 896–1226（331 aa） Fragment：ACTIVATION DOMAIN, RESIDUES 897 - 1227
Not recorded ACT ACETATE ION × 1 SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.2
Resolution 1.80 Å R-free 0.257
3BUL E. coli I690C/G743C MetH C-terminal fragment (649-1227) Deposited 2008-01-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 649–1227（579 aa） Fragment：C-terminal activation complex (residues 649-1227)
Mutation：I690C, G743C B12 COBALAMIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.2；310 K；0.2 M potassium nitrate, and 20 % (w/v) PEG3350, pH 7.2, EVAPORATION, temperature 310K
Resolution 2.30 Å R-free 0.247
3IV9 Structure of the B12-dependent Methionine Synthase (MetH) C-teminal half in a "His-On" conformation Deposited 2009-08-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 649–1227（579 aa） Fragment：C-terminal activation complex (UNP residues 649-1227)
Mutation：I690C, G743C B12 COBALAMIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；302 K；0.2 M potassium nitrate, 20 % (w/v) PEG3350, 50 mM HEPES pH 7.5, VAPOR DIFFUSION, temperature 302K
Resolution 3.25 Å R-free 0.321
3IVA Structure of the B12-dependent Methionine Synthase (MetH) C-teminal half with AdoHcy bound Deposited 2009-08-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 649–1227（579 aa） Fragment：C-terminal activation complex (UNP residues 649-1227)
Mutation：I690C, G743C B12 COBALAMIN × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 NO3 NITRATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；302 K；0.2 M potassium nitrate, 18 % (w/v) PEG3350, pH 7.0, VAPOR DIFFUSION, temperature 302K
Resolution 2.70 Å R-free 0.300
6BM5 Crystal Structure of the MetH Reactivation Domain bound to AdoMet Deposited 2017-11-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 897–1227（331 aa） Fragment：reactivation domain
Not recorded SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；28% PEG 6000, 100mM Tris pH 7.4, 300mM magnesium acetate:15mg/mL protein, 3mM AdoMet, 10mM Tris 7.2, 10mM EDTA, 3:3uL
Resolution 1.50 Å R-free 0.194
6BM6 Crystal Structure of the MetH Reactivation Domain bound to AdoHcy Deposited 2017-11-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 897–1227（331 aa） Fragment：reactivation domain
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；27-32% PEG 6000, 100mM Tris pH 7.2-7.5, 300mM magnesium acetate:15mg/mL protein, 5mM AdoHcy, 20mM Tris 7.2, 20mM EDTA, 2:2uL
Resolution 1.50 Å R-free 0.204

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name METH_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–333； UniProt 897–1227

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 6bdy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6bdy
Deposition date deposition_date2017-10-24
Structure title titleCrystal Structure of the MetH Reactivation Domain bound to Sinefungin
Keywords keywordsC-terminal domain, reactivation domain, MetH-sinefungin, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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_guinier21.86 Å
Radius of gyration Rg (electron density) rg_electron20.83 Å
Forward intensity I(0) i023348600.00
Molecular weight molecular_weight36585.0 kDa
Excluded volume excluded_volume45503 ų
Envelope volume envelope_volume52733 ų
Hydration-shell volume shell_volume21293 ų
Envelope diameter envelope_diameter69.7 Å
Shell Rg shell_rg27.44 Å
Envelope Rg envelope_rg21.07 Å
Shape Rg shape_rg20.82 Å
Total Rg total_rg21.70 Å
Total atoms total_atoms2590
Residues n_residues326
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 dmax68.3 Å
Rg (real space) rg_real21.80 Å
Rg uncertainty (real space) rg_real_error0.35 Å
I(0) (real space) i0_real2.3350e+07
I(0) uncertainty (real space) i0_real_error2.4390e+05
Rg (reciprocal space) rg_reciprocal21.82 Å
I(0) (reciprocal space) i0_reciprocal23350000.0000
Solution quality estimate total_estimate0.9087
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.5 Å
Skewness Skewness skewness0.254
Kurtosis Kurtosis kurtosis-0.498
Angular range angular_range— – 0.3650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5261000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.988
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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) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6bdya_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.173 — Methionine synthase activation domain-like
Superfamily Superfamily superfamilyd.173.1 — Methionine synthase activation domain-like
Family Family familyd.173.1.1 — Methionine synthase SAM-binding domain

CATH v4.4 (2 domains)

Domain ID domain_id6bdyA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology196 — Cobalamin-dependent Methionine Synthase; domain 1
Homologous superfamily homologous superfamily10 — Vitamin B12-dependent methionine synthase, activation domain
Domain ID domain_id6bdyA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology288 — Cobalamin-dependent Methionine Synthase; domain 2
Homologous superfamily homologous superfamily10 — Cobalamin-dependent Methionine Synthase, domain 2
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8. Citations (1)

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9. Files and Curves (10)