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- PDB-1bmt: HOW A PROTEIN BINDS B12: A 3.O ANGSTROM X-RAY STRUCTURE OF THE B1... -

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Basic information

Entry
Database: PDB / ID: 1bmt
TitleHOW A PROTEIN BINDS B12: A 3.O ANGSTROM X-RAY STRUCTURE OF THE B12-BINDING DOMAINS OF METHIONINE SYNTHASE
ComponentsMETHIONINE SYNTHASE
KeywordsMETHYLTRANSFERASE
Function / homology
Function and homology information


methionine synthase / methionine synthase activity / homocysteine metabolic process / methionine biosynthetic process / cobalamin binding / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / methylation / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Methionine synthase domain / Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12 dependent methionine synthase, activation domain / AdoMet activation domain profile. / Cobalamin-dependent methionine synthase / Methionine synthase, B12-binding domain / Vitamin B12-dependent methionine synthase, activation domain superfamily / B12-binding N-terminal domain profile. / B12 binding domain / Homocysteine-binding domain ...Methionine synthase domain / Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12 dependent methionine synthase, activation domain / AdoMet activation domain profile. / Cobalamin-dependent methionine synthase / Methionine synthase, B12-binding domain / Vitamin B12-dependent methionine synthase, activation domain superfamily / B12-binding N-terminal domain profile. / B12 binding domain / Homocysteine-binding domain / Homocysteine-binding domain superfamily / Homocysteine S-methyltransferase / Homocysteine-binding domain profile. / Cobalamin-binding domain / : / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CO-METHYLCOBALAMIN / Methionine synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsDrennan, C.L. / Huang, S. / Drummond, J.T. / Matthews, R.G. / Ludwig, M.L.
Citation
Journal: Science / Year: 1994
Title: How a protein binds B12: A 3.0 A X-ray structure of B12-binding domains of methionine synthase.
Authors: Drennan, C.L. / Huang, S. / Drummond, J.T. / Matthews, R.G. / Ludwig, M.L.
#1: Journal: Curr.Opin.Struct.Biol. / Year: 1994
Title: Cobalamin-Dependent Methionine Synthase: The Structure of a Methylcobalamin-Binding Fragment and Implications for Other B12-Dependent Enzymes
Authors: Drennan, C.L. / Matthews, R.G. / Ludwig, M.L.
History
DepositionSep 2, 1994Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 27, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / database_2 / entity_src_gen / pdbx_database_status / struct_site
Item: _citation.pdbx_database_id_DOI / _citation_author.name ..._citation.pdbx_database_id_DOI / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHIONINE SYNTHASE
B: METHIONINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1074
Polymers54,4182
Non-polymers2,6892
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.700, 55.300, 103.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein METHIONINE SYNTHASE


Mass: 27209.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P13009, methionine synthase
#2: Chemical ChemComp-COB / CO-METHYLCOBALAMIN


Mass: 1344.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H91CoN13O14P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SECONDARY STRUCTURAL ELEMENTS WERE IDENTIFIED BY HYDROGEN BONDING PATTERNS AND THE METHOD OF ...THE SECONDARY STRUCTURAL ELEMENTS WERE IDENTIFIED BY HYDROGEN BONDING PATTERNS AND THE METHOD OF KABSCH AND SANDER, 1983.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
250 mMTris-HCl11
1PEG600011

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 10417 / % possible obs: 89 % / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.17 -
obs0.17 9019
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 184 2 4000
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.61
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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