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

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Basic information

Entry
Database: PDB / ID: 5dmm
TitleCrystal Structure of the Homocysteine Methyltransferase MmuM from Escherichia coli, Metallated 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-homocysteine S-methyltransferase activity / S-methylmethionine cycle / 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
BETA-MERCAPTOETHANOL / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / Homocysteine S-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.779 Å
AuthorsLi, K. / Li, G. / Bradbury, L.M.T. / Andrew, H.D. / Bruner, S.D.
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 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Apr 3, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.5May 1, 2024Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id

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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)33,8676
Polymers33,4581
Non-polymers4105
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-52 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.949, 85.924, 87.662
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-636-

HOH

21A-724-

HOH

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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 / Production host: Escherichia coli (E. coli) / Strain (production host): C43
References: UniProt: Q47690, homocysteine S-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.93 % / Description: rod-shaped
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.6 M ammonium sulphate, 10% v/v glycerol and 0.1 M sodium acetate pH 4.8
PH range: 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 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: 1.779→24.23 Å / Num. obs: 13523 / % possible obs: 93.4 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.093 / Rsym value: 0.104 / Net I/σ(I): 14.86
Reflection shellResolution: 1.779→1.84 Å / Redundancy: 5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.49 / % possible all: 95.36

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSDarwin 13.4.0data reduction
Aimless0.5.8data scaling
ARP3.3.1model building
MOLREP2.12phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1q7m

1q7m


Resolution: 1.779→24.225 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 1427 5.28 %Random selection
Rwork0.183 ---
obs0.1841 -93.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.779→24.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 15 180 2366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072238
X-RAY DIFFRACTIONf_angle_d1.1193047
X-RAY DIFFRACTIONf_dihedral_angle_d14.163801
X-RAY DIFFRACTIONf_chiral_restr0.044349
X-RAY DIFFRACTIONf_plane_restr0.006402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7793-1.84290.28381720.25732538X-RAY DIFFRACTION95
1.8429-1.91660.27991130.23972683X-RAY DIFFRACTION97
1.9166-2.00380.22141510.21312575X-RAY DIFFRACTION96
2.0038-2.10940.21021220.19852614X-RAY DIFFRACTION96
2.1094-2.24150.21561790.18482561X-RAY DIFFRACTION95
2.2415-2.41440.20951450.18452570X-RAY DIFFRACTION95
2.4144-2.65710.20341400.19162558X-RAY DIFFRACTION93
2.6571-3.0410.22291480.18672543X-RAY DIFFRACTION92
3.041-3.82890.19461120.16112520X-RAY DIFFRACTION90
3.8289-24.22690.16361450.15692436X-RAY DIFFRACTION85

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