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- PDB-1kia: Crystal structure of glycine N-methyltransferase complexed with S... -

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Basic information

Entry
Database: PDB / ID: 1kia
TitleCrystal structure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate
ComponentsGlycine N-methyltransferase
KeywordsTRANSFERASE / Glycine N-methyltransferase / S-adenosylmethionine / Acetate / Ternary complex
Function / homology
Function and homology information


selenol Se-methyltransferase activity / Glyoxylate metabolism and glycine degradation / glycine N-methyltransferase / sarcosine metabolic process / glycine N-methyltransferase activity / methyltransferase complex / methionine metabolic process / S-adenosylhomocysteine metabolic process / glycine metabolic process / S-adenosylmethionine metabolic process ...selenol Se-methyltransferase activity / Glyoxylate metabolism and glycine degradation / glycine N-methyltransferase / sarcosine metabolic process / glycine N-methyltransferase activity / methyltransferase complex / methionine metabolic process / S-adenosylhomocysteine metabolic process / glycine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding / folic acid binding / glycine binding / regulation of gluconeogenesis / glycogen metabolic process / S-adenosylmethionine-dependent methyltransferase activity / one-carbon metabolic process / methylation / protein homotetramerization / identical protein binding / cytosol
Similarity search - Function
Glycine N-methyltransferase; chain A, domain 1 / Glycine N-methyltransferase, chain A, domain 1 / Glycine/Sarcosine N-methyltransferase / Glycine N-methyltransferase (EC 2.1.1.20 and EC 2.1.1.156) family profile. / Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich ...Glycine N-methyltransferase; chain A, domain 1 / Glycine N-methyltransferase, chain A, domain 1 / Glycine/Sarcosine N-methyltransferase / Glycine N-methyltransferase (EC 2.1.1.20 and EC 2.1.1.156) family profile. / Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / S-ADENOSYLMETHIONINE / Glycine N-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTakusagawa, F. / Huang, Y.
CitationJournal: To be Published
Title: Crystal structure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate
Authors: Takusagawa, F. / Huang, Y.
History
DepositionDec 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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

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Assembly

Deposited unit
A: Glycine N-methyltransferase
B: Glycine N-methyltransferase
C: Glycine N-methyltransferase
D: Glycine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,67312
Polymers129,8434
Non-polymers1,8308
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.95, 117.01, 137.78
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homotetramer. The residues 1 - 17 of each subunit are disordered.

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Components

#1: Protein
Glycine N-methyltransferase / / Folate-binding protein


Mass: 32460.830 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P13255, glycine N-methyltransferase
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


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


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 1, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 252252 / Num. obs: 252116 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 24.2
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 5 / Num. unique all: 3543 / Rsym value: 0.324 / % possible all: 96.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The residues 1 - 17 of each subunit are disordered.
RfactorNum. reflectionSelection details
Rfree0.286 3132 RANDOM
Rwork0.216 --
all0.225 33065 -
obs0.221 28280 -
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8640 0 124 235 8999
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d27
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs
2.8-2.920.3283420.2630.022859
2.92-3.070.3333440.2530.0183208
3.48-3.790.2744130.210.0133691
3.79-4.270.2443810.1880.0123798
4.27-5.130.2434260.1720.0123856
5.13-80.3274400.2460.0123906

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