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- PDB-1r8y: Crystal Structure of Mouse Glycine N-Methyltransferase (Monoclini... -

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Basic information

Entry
Database: PDB / ID: 1r8y
TitleCrystal Structure of Mouse Glycine N-Methyltransferase (Monoclinic Form)
Componentsglycine N-methyltransferase
KeywordsTRANSFERASE / Glycine N-Methyltransferase
Function / homology
Function and homology information


glycine N-methyltransferase / Glyoxylate metabolism and glycine degradation / glycine N-methyltransferase activity / methionine metabolic process / S-adenosylmethionine metabolic process / folic acid binding / regulation of gluconeogenesis / glycogen metabolic process / glycine binding / one-carbon metabolic process ...glycine N-methyltransferase / Glyoxylate metabolism and glycine degradation / glycine N-methyltransferase activity / methionine metabolic process / S-adenosylmethionine metabolic process / 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 / 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 / MIR / Resolution: 3 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: 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
C: glycine N-methyltransferase
D: glycine N-methyltransferase
E: glycine N-methyltransferase
F: glycine N-methyltransferase
G: glycine N-methyltransferase
H: glycine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,47818
Polymers260,6968
Non-polymers78110
Water25214
1
A: glycine N-methyltransferase
B: glycine N-methyltransferase
C: glycine N-methyltransferase
D: glycine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,81710
Polymers130,3484
Non-polymers4696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14720 Å2
ΔGint-57 kcal/mol
Surface area46810 Å2
MethodPISA
2
E: glycine N-methyltransferase
F: glycine N-methyltransferase
G: glycine N-methyltransferase
H: glycine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,6618
Polymers130,3484
Non-polymers3134
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14110 Å2
ΔGint-61 kcal/mol
Surface area46510 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29650 Å2
ΔGint-119 kcal/mol
Surface area92500 Å2
MethodPISA
4
A: glycine N-methyltransferase
B: glycine N-methyltransferase
C: glycine N-methyltransferase
D: glycine N-methyltransferase
hetero molecules

E: glycine N-methyltransferase
F: glycine N-methyltransferase
G: glycine N-methyltransferase
H: glycine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,47818
Polymers260,6968
Non-polymers78110
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area29590 Å2
ΔGint-119 kcal/mol
Surface area92560 Å2
MethodPISA
5
A: glycine N-methyltransferase
B: glycine N-methyltransferase
C: glycine N-methyltransferase
D: glycine N-methyltransferase
hetero molecules

E: glycine N-methyltransferase
F: glycine N-methyltransferase
G: glycine N-methyltransferase
H: glycine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,47818
Polymers260,6968
Non-polymers78110
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area29580 Å2
ΔGint-120 kcal/mol
Surface area92570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.980, 108.300, 119.010
Angle α, β, γ (deg.)90.00, 93.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

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
11THRTHRGLNGLNAA7 - 2237 - 223
21THRTHRVALVALBB7 - 2247 - 224
31THRTHRVALVALCC7 - 2247 - 224
41THRTHRVALVALDD7 - 2247 - 224
51THRTHRVALVALEE7 - 2247 - 224
61THRTHRVALVALFF7 - 2247 - 224
71THRTHRVALVALGG7 - 2247 - 224
81THRTHRVALVALHH7 - 2247 - 224
12SERSERTHRTHRAA236 - 291236 - 291
22SERSERTHRTHRBB236 - 291236 - 291
32SERSERLYSLYSCC236 - 290236 - 290
42SERSERTHRTHRDD236 - 291236 - 291
52SERSERTHRTHREE236 - 291236 - 291
62SERSERTHRTHRFF236 - 291236 - 291
72SERSERTHRTHRGG236 - 291236 - 291
82SERSERTHRTHRHH236 - 291236 - 291
DetailsThe biological assembly is a tetramer

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Components

#1: Protein
glycine N-methyltransferase


Mass: 32587.029 Da / Num. of mol.: 8
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


Mass: 78.133 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.66 Å3/Da / Density % sol: 53.81 %
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 FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 9, 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: 3→30 Å / Num. all: 40592 / Num. obs: 40592 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.066 / Net I/σ(I): 19.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.05 / Num. unique all: 5137 / Rsym value: 0.403 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIR
Starting model: PDB entry 1XVA

1xva


Resolution: 3→13 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.878 / SU B: 28.246 / SU ML: 0.501 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.641 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28508 1217 3 %RANDOM
Rwork0.22215 ---
all0.224 39000 --
obs0.224 39000 74.16 %-
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: 24.658 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å20 Å20.37 Å2
2--0.99 Å20 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 3→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17552 0 40 14 17606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02118012
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.651.94224428
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.75552249
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_restr0.1120.22678
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213780
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.27745
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2552
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3910.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.3531.511219
X-RAY DIFFRACTIONr_mcangle_it0.662217896
X-RAY DIFFRACTIONr_scbond_it1.09136793
X-RAY DIFFRACTIONr_scangle_it1.6274.56532
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1807 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.070.05
2Btight positional0.070.05
3Ctight positional0.060.05
4Dtight positional0.070.05
5Etight positional0.080.05
6Ftight positional0.070.05
7Gtight positional0.070.05
8Htight positional0.070.05
1Atight thermal0.120.5
2Btight thermal0.110.5
3Ctight thermal0.10.5
4Dtight thermal0.120.5
5Etight thermal0.120.5
6Ftight thermal0.110.5
7Gtight thermal0.120.5
8Htight thermal0.120.5
LS refinement shellResolution: 3→3.074 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.465 87
Rwork0.346 2753
obs-2753
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.43010.10770.40442.11180.96793.0375-0.03690.13470.08580.3865-0.01090.60210.3712-0.240.04780.17340.01240.15480.20780.07180.47173.007100.139578.6918
23.31080.5313-0.67420.33590.8254.33820.16010.02650.1678-0.23880.010.4243-0.08780.1529-0.17010.29250.1192-0.23280.4215-0.01280.4329-0.781794.015843.0353
35.9980.303-1.63571.7669-0.33694.72350.29431.06690.4805-0.3503-0.2084-0.3663-0.0012-0.304-0.08590.16910.16880.05440.50730.05650.230644.6559100.07238.3933
44.9131-0.6421-0.80350.836-0.35933.84220.0114-0.44330.18030.23070.0046-0.2381-0.10160.457-0.0160.1950.0759-0.14990.356-0.20710.18348.775896.337774.257
50.6674-0.0935-0.07784.8356-2.18544.6574-0.1498-0.21590.00550.13520.51410.40920.335-0.3401-0.36430.3318-0.0543-0.07270.1670.08910.235375.473275.729419.6407
60.8970.1925-1.70623.2876-0.77625.3259-0.37870.4262-0.3648-0.4186-0.131-0.25371.4512-0.31050.50960.7722-0.03710.01010.3034-0.06090.311387.105472.3854-14.6271
71.0014-0.8581-0.15053.90450.22823.8880.16470.32540.3086-0.214-0.0952-0.0758-0.16330.2112-0.06940.0636-0.06070.04860.18140.13120.460783.6512117.9068-19.9125
80.94660.07980.2194.6030.19994.2647-0.0759-0.22170.25570.4809-0.0102-0.048-0.2838-0.2120.08610.21930.04430.01810.1301-0.10110.456480.7274121.18316.146
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2922 - 292
2X-RAY DIFFRACTION1AI1262
3X-RAY DIFFRACTION1AJ1282
4X-RAY DIFFRACTION2BB2 - 2922 - 292
5X-RAY DIFFRACTION2BK2057
6X-RAY DIFFRACTION3CC2 - 2902 - 290
7X-RAY DIFFRACTION4DD2 - 2922 - 292
8X-RAY DIFFRACTION4DL4185
9X-RAY DIFFRACTION4DM4246
10X-RAY DIFFRACTION4DN4262
11X-RAY DIFFRACTION5EE2 - 2922 - 292
12X-RAY DIFFRACTION5EO5246
13X-RAY DIFFRACTION6FF2 - 2912 - 291
14X-RAY DIFFRACTION6FP6282
15X-RAY DIFFRACTION7GG2 - 2922 - 292
16X-RAY DIFFRACTION7GQ7246
17X-RAY DIFFRACTION7GR7282
18X-RAY DIFFRACTION8HH2 - 2922 - 292

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