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- PDB-1msk: METHIONINE SYNTHASE (ACTIVATION DOMAIN) -

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Basic information

Entry
Database: PDB / ID: 1msk
TitleMETHIONINE SYNTHASE (ACTIVATION DOMAIN)
ComponentsCOBALAMIN-DEPENDENT METHIONINE SYNTHASE
KeywordsMETHYLTRANSFERASE / TRANSFERASE / METHIONINE BIOSYNTHESIS / VITAMIN B12
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
Cobalamin-dependent Methionine Synthase; domain 2 / Cobalamin-dependent Methionine Synthase, domain 2 / Cobalamin-dependent Methionine Synthase; domain 1 / Vitamin B12-dependent methionine synthase, activation 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 ...Cobalamin-dependent Methionine Synthase; domain 2 / Cobalamin-dependent Methionine Synthase, domain 2 / Cobalamin-dependent Methionine Synthase; domain 1 / Vitamin B12-dependent methionine synthase, activation 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 (vitamin B12)-binding module, cap domain / B12 binding domain / 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 / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / S-ADENOSYLMETHIONINE / Methionine synthase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.8 Å
AuthorsDixon, M.M. / Huang, S. / Matthews, R.G. / Ludwig, M.L.
Citation
Journal: Structure / Year: 1996
Title: The structure of the C-terminal domain of methionine synthase: presenting S-adenosylmethionine for reductive methylation of B12.
Authors: Dixon, M.M. / Huang, S. / Matthews, R.G. / Ludwig, M.
#1: 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.
History
DepositionAug 3, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COBALAMIN-DEPENDENT METHIONINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2073
Polymers37,7491
Non-polymers4572
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.860, 62.360, 140.820
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 COBALAMIN-DEPENDENT METHIONINE SYNTHASE


Mass: 37749.168 Da / Num. of mol.: 1 / Fragment: ACTIVATION DOMAIN, RESIDUES 897 - 1227 / Source method: isolated from a natural source
Details: GENERATED BY TRYPSIN CLEAVAGE OF THE METHIONINE SYNTHASE HOLOENZYME
Source: (natural) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12, DH5AF'-P4B6.3 / References: UniProt: P13009, methionine synthase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ACTIVATION DOMAIN WAS GENERATED BY TRYPSIN CLEAVAGE OF THE METHIONINE SYNTHASE HOLOENZYME.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 46 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
210 mMTris-HCl1drop
310 mMEDTA1drop
430 %PEG60001reservoir
5300 mMMgAcetate1reservoir
6100 mMTris-HCl1reservoir
74-5 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: ADSC / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 28762 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.0532 / Net I/σ(I): 10.1

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
ADSCdata collection
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→10 Å / σ(F): 0
Details: TWO LOOPS, CONSISTING OF RESIDUES 965 - 967 AND 1035 - 1036, ARE DISORDERED, WITH AVERAGE MAIN-CHAIN B-FACTORS > 50.0 A**2. THREE RESIDUES AT THE C-TERMINAL END, 1225 - 1227, ARE DISORDERED, ...Details: TWO LOOPS, CONSISTING OF RESIDUES 965 - 967 AND 1035 - 1036, ARE DISORDERED, WITH AVERAGE MAIN-CHAIN B-FACTORS > 50.0 A**2. THREE RESIDUES AT THE C-TERMINAL END, 1225 - 1227, ARE DISORDERED, WITH AVERAGE MAIN-CHAIN B-FACTORS > 50.0 A**2.
RfactorNum. reflection% reflection
Rfree0.257 -10 %
Rwork0.198 --
obs0.198 28445 -
Displacement parametersBiso mean: 21.94 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 31 212 2873
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg1.84
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.69
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.69

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