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- PDB-2azt: Crystal structure of H176N mutant of human Glycine N-Methyltransferase -

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Basic information

Entry
Database: PDB / ID: 2azt
TitleCrystal structure of H176N mutant of human Glycine N-Methyltransferase
ComponentsGlycine N-methyltransferase
KeywordsTRANSFERASE / glycine N-methyltransferase
Function / homology
Function and homology information


glycine N-methyltransferase / sarcosine metabolic process / glycine N-methyltransferase activity / methionine metabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding / Glyoxylate metabolism and glycine degradation / folic acid binding ...glycine N-methyltransferase / sarcosine metabolic process / glycine N-methyltransferase activity / methionine metabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding / Glyoxylate metabolism and glycine degradation / folic acid binding / glycine binding / regulation of gluconeogenesis / glycogen metabolic process / protein modification 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
BETA-MERCAPTOETHANOL / CITRIC ACID / Glycine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLuka, Z. / Pakhomova, S. / Luka, Y. / Newcomer, M.E. / Wagner, C.
CitationJournal: Protein Sci. / Year: 2007
Title: Destabilization of human glycine N-methyltransferase by H176N mutation.
Authors: Luka, Z. / Pakhomova, S. / Luka, Y. / Newcomer, M.E. / Wagner, C.
History
DepositionSep 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,33110
Polymers65,5202
Non-polymers8108
Water72140
1
A: Glycine N-methyltransferase
B: Glycine N-methyltransferase
hetero molecules

A: Glycine N-methyltransferase
B: Glycine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,66220
Polymers131,0414
Non-polymers1,62116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-x+2,-y-1,z1
Buried area15720 Å2
ΔGint-81 kcal/mol
Surface area45930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.116, 83.279, 115.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer. The second part of the biological assembly is generated by the two fold axis: -x+2,-y-1,z

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Components

#1: Protein Glycine N-methyltransferase /


Mass: 32760.211 Da / Num. of mol.: 2 / Mutation: H176N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNMT / Plasmid: pGE3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q14749, glycine N-methyltransferase
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.8
Details: 10% PEG4000, 0.1M Na citrate, 5% glycerol, pH 5.8, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 3, 2002 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. all: 21138 / Num. obs: 21138 / % possible obs: 96.2 % / Observed criterion σ(F): -3 / Redundancy: 4.5 % / Rsym value: 0.058 / Net I/σ(I): 28.6
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 2015 / Rsym value: 0.379 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1R74

1r74


Resolution: 2.7→13 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.868 / SU ML: 0.278 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.119 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28172 1369 6.7 %RANDOM
Rwork0.23599 ---
all0.23918 18950 --
obs0.23918 18950 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.855 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.63 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.7→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 47 40 4355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214419
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.955981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.865547
X-RAY DIFFRACTIONr_chiral_restr0.1340.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023365
X-RAY DIFFRACTIONr_nbd_refined0.2410.21845
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.26
X-RAY DIFFRACTIONr_mcbond_it0.5921.52738
X-RAY DIFFRACTIONr_mcangle_it1.06124359
X-RAY DIFFRACTIONr_scbond_it1.94131681
X-RAY DIFFRACTIONr_scangle_it2.5454.51622
LS refinement shellResolution: 2.7→2.767 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.498 95
Rwork0.392 1319
obs-1319

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