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- PDB-1r8x: Crystal Structure of Mouse Glycine N-Methyltransferase (Tetragona... -

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Basic information

Entry
Database: PDB / ID: 1r8x
TitleCrystal Structure of Mouse Glycine N-Methyltransferase (Tetragonal Form)
Componentsglycine N-methyltransferase
KeywordsTRANSFERASE / Glycine N-Methyltransferase
Function / homology
Function and homology information


glycine N-methyltransferase / sarcosine metabolic process / glycine N-methyltransferase activity / methyltransferase complex / Glyoxylate metabolism and glycine degradation / methionine metabolic process / S-adenosylhomocysteine metabolic process / glycine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding ...glycine N-methyltransferase / sarcosine metabolic process / glycine N-methyltransferase activity / methyltransferase complex / Glyoxylate metabolism and glycine degradation / methionine metabolic process / S-adenosylhomocysteine metabolic process / glycine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding / glycogen metabolic process / folic acid binding / glycine binding / regulation of gluconeogenesis / S-adenosylmethionine-dependent methyltransferase activity / 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 / 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 / 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 / Glycine N-methyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 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 28, 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)65,7318
Polymers65,1742
Non-polymers5576
Water37821
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)131,46216
Polymers130,3484
Non-polymers1,11412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+3/21
Buried area17210 Å2
ΔGint-56 kcal/mol
Surface area44710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.700, 70.700, 266.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPTYRTYRAA2 - 2202 - 220
112ASPASPTYRTYRBB2 - 2202 - 220
121LEULEULYSLYSAA240 - 290240 - 290
122LEULEULYSLYSBB240 - 290240 - 290
211TRSTRSTRSTRSAE1247
212TRSTRSTRSTRSBH2263

NCS ensembles :
ID
1
2
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: -y,-x,-z+1.5

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Components

#1: Protein glycine N-methyltransferase /


Mass: 32587.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: GNMT / Plasmid: pET17b, pMME / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9QXF8
#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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: PEG4000, isopropanol, Tris, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 17, 2002 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 14973 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rsym value: 0.068 / Net I/σ(I): 6.7
Reflection shellResolution: 2.95→3.05 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.431 / % possible all: 99.7

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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
Resolution: 2.95→10.5 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.882 / SU B: 24.137 / SU ML: 0.427 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27266 823 5.6 %RANDOM
Rwork0.20678 ---
all0.21048 14973 --
obs0.21048 13784 99.77 %-
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: 27.202 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20 Å20 Å2
2--1.67 Å20 Å2
3----3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.95→10.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4356 0 32 21 4409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0214490
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1671.9446092
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2645563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1340.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023430
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2550.21985
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2156
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6941.52816
X-RAY DIFFRACTIONr_mcangle_it1.30824484
X-RAY DIFFRACTIONr_scbond_it2.0831674
X-RAY DIFFRACTIONr_scangle_it3.2184.51608
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
111985tight positional0.090.05
128tight positional0.090.05
211985tight thermal0.20.5
228tight thermal0.160.5
LS refinement shellResolution: 2.95→3.02 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.37 79
Rwork0.329 893
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
1-1.0724-0.6749-0.3163-0.02861.550614.5881-0.20630.3166-0.0568-0.18580.1015-0.11730.88710.84850.10480.5076-0.0201-0.04560.4471-0.250.510412.12055.6263202.6947
22.851.07172.11722.32373.274416.69420.20950.27170.5559-0.90910.2485-0.12-3.55861.3118-0.45811.3487-0.370.39140.3159-0.03020.615117.931825.0712182.7507
35.36834.36051.81674.54671.45837.00270.5480.6263-0.5636-0.57540.1257-0.91360.33531.5769-0.67370.52750.10080.06330.5079-0.20910.47814.24035.6757179.7289
43.38760.94730.2085-2.74661.94648.9173-0.09010.68030.1015-0.3174-0.00890.0068-0.6914-1.42590.0990.53530.0053-0.03360.5081-0.11240.47066.416812.2609199.6745
53.7972.5936-0.28383.31480.22826.40050.0755-0.5002-0.0090.08120.5026-0.5057-0.19721.0209-0.57810.11230.0822-0.04760.653-0.46450.482721.884313.554223.701
66.76114.09590.39476.15333.047.43910.0463-0.54810.67310.01540.00260.3457-0.5267-0.7945-0.04890.05130.10680.01060.504-0.27080.30651.769110.9224221.9445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 372 - 37
2X-RAY DIFFRACTION2AA38 - 17838 - 178
3X-RAY DIFFRACTION2AA246 - 292246 - 292
4X-RAY DIFFRACTION2AC1146
5X-RAY DIFFRACTION2BF2146
6X-RAY DIFFRACTION2AE1247
7X-RAY DIFFRACTION3AA179 - 245179 - 245
8X-RAY DIFFRACTION4BB2 - 372 - 37
9X-RAY DIFFRACTION5BB38 - 17838 - 178
10X-RAY DIFFRACTION5BB246 - 292246 - 292
11X-RAY DIFFRACTION5AD1246
12X-RAY DIFFRACTION5BG2262
13X-RAY DIFFRACTION5BH2263
14X-RAY DIFFRACTION6BB179 - 245179 - 245

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