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- PDB-1d2c: METHYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1d2c
TitleMETHYLTRANSFERASE
ComponentsPROTEIN (GLYCINE N-METHYLTRANSFERASE)
KeywordsTRANSFERASE / METHYLTRANSFERASE
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 / glycine metabolic process / S-adenosylhomocysteine 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 / glycine metabolic process / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / folic acid binding / regulation of gluconeogenesis / glycogen metabolic process / glycine binding / one-carbon metabolic process / protein homotetramerization / methylation / 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
Glycine N-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsHuang, Y. / Takusagawa, F.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Mechanisms for auto-inhibition and forced product release in glycine N-methyltransferase: crystal structures of wild-type, mutant R175K and S-adenosylhomocysteine-bound R175K enzymes.
Authors: Huang, Y. / Komoto, J. / Konishi, K. / Takata, Y. / Ogawa, H. / Gomi, T. / Fujioka, M. / Takusagawa, F.
History
DepositionSep 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GLYCINE N-METHYLTRANSFERASE)
B: PROTEIN (GLYCINE N-METHYLTRANSFERASE)


Theoretical massNumber of molelcules
Total (without water)64,9222
Polymers64,9222
Non-polymers00
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-17 kcal/mol
Surface area26120 Å2
MethodPISA
2
A: PROTEIN (GLYCINE N-METHYLTRANSFERASE)
B: PROTEIN (GLYCINE N-METHYLTRANSFERASE)

A: PROTEIN (GLYCINE N-METHYLTRANSFERASE)
B: PROTEIN (GLYCINE N-METHYLTRANSFERASE)


Theoretical massNumber of molelcules
Total (without water)129,8434
Polymers129,8434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area13330 Å2
ΔGint-49 kcal/mol
Surface area47580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.300, 175.900, 45.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

DetailsTWO SUBUNITS ARE IN AN ASYMMETRIC UNIT. THE TETRAMERIC ENZYME CAN BE GENERATED BY THE FOLLOWING CRYSTALLOGRAPHIC SYMMETRY OPERATION: 2-X, 1-Y, Z,

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Components

#1: Protein PROTEIN (GLYCINE N-METHYLTRANSFERASE) / GNMT / S-ADENOSYL-L-METHIONINE:GLYCINE METHYLTRANSFERASE


Mass: 32460.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: LIVER / Production host: Escherichia coli (E. coli) / References: UniProt: P13255, glycine N-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.6
Details: PEG 3400, pH 5.6, VAPOR DIFFUSION, temperature 4.0K
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMsodium citrate1drop
2100 mMammonium acetate1drop
350 mM1dropNaCl
413 %(w/v)PEG40001drop
510 mg/mlprotain1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 11, 1998
RadiationMonochromator: GRAPHITE (0 0 2 ) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 69713 / Num. obs: 22488 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 3.15
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.98 / Num. unique all: 22488 / % possible all: 92.2
Reflection
*PLUS
Num. measured all: 69713
Reflection shell
*PLUS
Mean I/σ(I) obs: 3.15

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.5→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2250 -random
Rwork0.175 ---
all0.175 69713 --
obs0.175 22488 92.2 %-
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 0 0 316 4886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.35
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8

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