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- PDB-1d2g: CRYSTAL STRUCTURE OF R175K MUTANT GLYCINE N-METHYLTRANSFERASE FRO... -

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Basic information

Entry
Database: PDB / ID: 1d2g
TitleCRYSTAL STRUCTURE OF R175K MUTANT GLYCINE N-METHYLTRANSFERASE FROM RAT LIVER
ComponentsGLYCINE N-METHYLTRANSFERASE
KeywordsTRANSFERASE / METHYLTRANSFERASE
Function / homology
Function and homology information


selenol Se-methyltransferase activity / Glyoxylate metabolism and glycine degradation / glycine N-methyltransferase / glycine N-methyltransferase activity / sarcosine metabolic process / 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 / glycine N-methyltransferase activity / sarcosine metabolic process / methyltransferase complex / methionine metabolic process / S-adenosylhomocysteine metabolic process / glycine metabolic process / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / folic acid binding / glycine binding / regulation of gluconeogenesis / glycogen metabolic process / 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
Glycine N-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsHuang, Y. / Komoto, J. / Takusagawa, F. / Konishi, K. / Takata, Y.
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
DepositionOct 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)64,8662
Polymers64,8662
Non-polymers00
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-19 kcal/mol
Surface area26230 Å2
MethodPISA
2
A: GLYCINE N-METHYLTRANSFERASE
B: GLYCINE N-METHYLTRANSFERASE

A: GLYCINE N-METHYLTRANSFERASE
B: GLYCINE N-METHYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)129,7314
Polymers129,7314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area13370 Å2
ΔGint-50 kcal/mol
Surface area48250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.7, 176.0, 45.5
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer constructed from chain A and B a symmetry partner generated by the two-fold.

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Components

#1: Protein GLYCINE N-METHYLTRANSFERASE /


Mass: 32432.818 Da / Num. of mol.: 2 / Fragment: WHOLE ENZYME / Mutation: R175K
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 / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG-4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
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: MACSCIENCE DIP100 / Detector: IMAGE PLATE / Date: Jan 10, 1997
RadiationProtocol: 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: 22390 / Num. obs: 22390 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 3.35
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.17 / Num. unique all: 2100 / % possible all: 85
Reflection
*PLUS
Lowest resolution: 10 Å / Num. measured all: 71872
Reflection shell
*PLUS
Mean I/σ(I) obs: 3.35

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
ELMSdata reduction
KUAVSTdata scaling
KUMDUdata scaling
X-PLORphasing
RefinementResolution: 2.5→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 --RANDOM
Rwork0.194 ---
all0.194 22390 --
obs0.194 22390 100 %-
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4566 0 0 318 4884
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
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_deg28.2

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