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- PDB-1r74: Crystal Structure of Human Glycine N-Methyltransferase -

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Basic information

Entry
Database: PDB / ID: 1r74
TitleCrystal Structure of Human Glycine N-Methyltransferase
ComponentsGlycine N-methyltransferase
KeywordsTRANSFERASE / Glycine N-Methyltransferase / human
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: 2.55 Å
AuthorsPakhomova, S. / Luka, Z. / Wagner, C. / Newcomer, M.E.
CitationJournal: Proteins / Year: 2004
Title: Glycine N-methyltransferases: a comparison of the crystal structures and kinetic properties of recombinant human, mouse and rat enzymes.
Authors: Pakhomova, S. / Luka, Z. / Grohmann, S. / Wagner, C. / Newcomer, M.E.
History
DepositionOct 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,0038
Polymers65,3062
Non-polymers6976
Water1,08160
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)132,00616
Polymers130,6124
Non-polymers1,39412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-x+2,-y-1,z1
Buried area15370 Å2
ΔGint-54 kcal/mol
Surface area45330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.840, 83.230, 114.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGPROPROAA6 - 1256 - 125
21ARGARGGLNGLNBB6 - 1266 - 126
32ASPASPVALVALAA133 - 224133 - 224
42ASPASPGLNGLNBB133 - 225133 - 225
53LEULEUTHRTHRAA237 - 293237 - 293
63LEULEUTHRTHRBB237 - 293237 - 293
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: -x+2,-y-1,z

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Components

#1: Protein Glycine N-methyltransferase /


Mass: 32653.062 Da / Num. of mol.: 2
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.: 4 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4000, Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 2, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→12 Å / Num. all: 23864 / Num. obs: 23864 / % possible obs: 98.3 % / Redundancy: 3.7 % / Rsym value: 0.051 / Net I/σ(I): 9.9
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.389 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XVA

1xva


Resolution: 2.55→12 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 11.27 / SU ML: 0.245 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.56 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26605 1623 6.9 %RANDOM
Rwork0.2218 ---
all0.2249 23864 --
obs0.22492 22070 98.37 %-
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: 29.659 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.55→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4240 0 42 60 4342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0214381
X-RAY DIFFRACTIONr_bond_other_d0.010.023904
X-RAY DIFFRACTIONr_angle_refined_deg2.1671.9465945
X-RAY DIFFRACTIONr_angle_other_deg1.60539038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8435549
X-RAY DIFFRACTIONr_chiral_restr0.1330.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.024929
X-RAY DIFFRACTIONr_gen_planes_other0.0330.02917
X-RAY DIFFRACTIONr_nbd_refined0.2420.2952
X-RAY DIFFRACTIONr_nbd_other0.2520.24270
X-RAY DIFFRACTIONr_nbtor_other0.10.22666
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3450.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4380.23
X-RAY DIFFRACTIONr_mcbond_it0.8621.52741
X-RAY DIFFRACTIONr_mcangle_it1.56824355
X-RAY DIFFRACTIONr_scbond_it2.58831640
X-RAY DIFFRACTIONr_scangle_it4.0034.51590
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3729 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.140.05
tight thermal0.210.5
LS refinement shellResolution: 2.55→2.613 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.397 135
Rwork0.323 1487
obs-1622

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