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- PDB-1bhj: CRYSTAL STRUCTURE OF APO-GLYCINE N-METHYLTRANSFERASE (GNMT) -

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Basic information

Entry
Database: PDB / ID: 1bhj
TitleCRYSTAL STRUCTURE OF APO-GLYCINE N-METHYLTRANSFERASE (GNMT)
ComponentsGLYCINE N-METHYLTRANSFERASE
KeywordsMETHYLTRANSFERASE / FOLATE BINDING PROTEIN
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 / 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 / RIGID BODY REFINEMENT / Resolution: 2.5 Å
AuthorsPattanayek, R. / Newcomer, M.E. / Wagner, C.
CitationJournal: Protein Sci. / Year: 1998
Title: Crystal structure of apo-glycine N-methyltransferase (GNMT).
Authors: Pattanayek, R. / Newcomer, M.E. / Wagner, C.
History
DepositionJun 9, 1998Processing site: BNL
Revision 1.0Jan 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 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)64,9222
Polymers64,9222
Non-polymers00
Water1,892105
1
A: GLYCINE N-METHYLTRANSFERASE
B: GLYCINE N-METHYLTRANSFERASE

A: GLYCINE N-METHYLTRANSFERASE
B: 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 area12680 Å2
ΔGint-58 kcal/mol
Surface area48480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.390, 174.210, 44.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein GLYCINE N-METHYLTRANSFERASE / GNMT / FOLATE BINDING PROTEIN


Mass: 32460.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: APO FORM / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Plasmid: PRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13255, glycine N-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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 growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Temperature: 11 ℃ / Method: vapor diffusion, hanging drop
Details: equal volume of protein and reservoir solution were used for the drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
210 mMTris-HCl1drop
31 mM1dropNaN3
410 mMbeta-mercaptoethanol1drop
52 mMdithiothreitol1drop
62 mMEDTA1drop
70.1 Msodium citrate1reservoir
81 Mammonium phosphate1reservoir
95 %glycerol1reservoir
10100 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 22481 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rsym value: 0.106 / Net I/σ(I): 10.59
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.73 / Rsym value: 0.417 / % possible all: 87
Reflection
*PLUS
Num. measured all: 254910 / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
% possible obs: 87 % / Rmerge(I) obs: 0.417

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: 1XVA

1xva


Resolution: 2.5→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1840 10 %RANDOM
Rwork0.221 ---
obs0.221 18688 78.7 %-
Displacement parametersBiso mean: 33.24 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 0 0 105 4675
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.325
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.77
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3183 184 10 %
Rwork0.221 1653 -
obs--53.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.77
LS refinement shell
*PLUS
Rfactor obs: 0.221

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