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- PDB-5dml: Crystal Structure of the Homocysteine Methyltransferase MmuM from... -

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Basic information

Entry
Database: PDB / ID: 5dml
TitleCrystal Structure of the Homocysteine Methyltransferase MmuM from Escherichia coli, Oxidized form
ComponentsHomocysteine S-methyltransferase
KeywordsTRANSFERASE / Homocysteine Methyltransferase
Function / homology
Function and homology information


homocysteine S-methyltransferase / S-adenosylmethionine-homocysteine S-methyltransferase activity / S-methylmethionine metabolic process / S-methylmethionine cycle / S-methylmethionine-homocysteine S-methyltransferase activity / methionine biosynthetic process / methylation / DNA damage response / zinc ion binding
Similarity search - Function
: / Betaine-homocysteine S-methyltransferase, BHMT / Homocysteine-binding-like domain / Homocysteine-binding domain / Homocysteine-binding domain superfamily / Homocysteine S-methyltransferase / Homocysteine-binding domain profile. / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Homocysteine S-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.452 Å
AuthorsLi, K. / Li, G. / Bradbury, L.M.T. / Andrew, H.D. / Bruner, S.D.
Funding support United States, 2items
OrganizationGrant numberCountry
University of Florida United States
National Science Foundation (NSF, United States)1153413 United States
CitationJournal: Biochem.J. / Year: 2016
Title: Crystal structure of the homocysteine methyltransferase MmuM from Escherichia coli.
Authors: Li, K. / Li, G. / Bradbury, L.M. / Hanson, A.D. / Bruner, S.D.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homocysteine S-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4932
Polymers33,4581
Non-polymers351
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.453, 84.463, 85.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Homocysteine S-methyltransferase / S-methylmethionine:homocysteine methyltransferase


Mass: 33457.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: mmuM, yagD, b0261, JW0253 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3)
References: UniProt: Q47690, homocysteine S-methyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 % / Description: rod-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 1.6 M ammonium sulphate, 10% v/v glycerol and 0.1 M sodium acetate pH 4.8
PH range: 4.6 - 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.452→34.39 Å / Num. obs: 10744 / % possible obs: 99.76 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.09589 / Rsym value: 0.1025 / Net I/σ(I): 18.19
Reflection shellResolution: 2.452→2.54 Å / Redundancy: 8 % / Rmerge(I) obs: 0.5965 / Mean I/σ(I) obs: 3.69 / % possible all: 97.69

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSOSX10.9.5_Darwin13.4.0data reduction
Aimless0.5.8data scaling
ARP3.3.1model building
MOLREP2.12phasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1q7m

1q7m


Resolution: 2.452→34.386 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.93 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.217 612 5.7 %
Rwork0.2022 --
obs0.2025 10744 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.452→34.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 0 1 32 2202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092216
X-RAY DIFFRACTIONf_angle_d1.2623024
X-RAY DIFFRACTIONf_dihedral_angle_d14.108781
X-RAY DIFFRACTIONf_chiral_restr0.062351
X-RAY DIFFRACTIONf_plane_restr0.008398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4564-2.70270.2521980.24722514X-RAY DIFFRACTION96
2.7027-3.09160.26811490.22782491X-RAY DIFFRACTION94
3.0916-3.8870.22151520.19042506X-RAY DIFFRACTION94
3.887-16.67540.19192070.18492556X-RAY DIFFRACTION93

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