[English] 日本語
Yorodumi
- PDB-1nbh: Structure of glycine N-methyltransferase complexed with S-adenosy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nbh
TitleStructure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate, GNMT:SAM:Ace
ComponentsGlycine N-methyltransferase
KeywordsTRANSFERASE / methyltransferase / Glycine N-methyltransferase / S-adenosylmethionine / Enzyme catalytic mechanism
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 / S-adenosylhomocysteine metabolic process / glycine 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 / S-adenosylhomocysteine metabolic process / glycine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding / S-adenosylmethionine-dependent methyltransferase activity / folic acid binding / glycine binding / regulation of gluconeogenesis / glycogen metabolic 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
ACETATE ION / S-ADENOSYLMETHIONINE / Glycine N-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTakata, Y. / Takusagawa, F.
CitationJournal: Biochemistry / Year: 2003
Title: Catalytic mechanism of glycine N-methyltransferase
Authors: Takata, Y. / Huang, Y. / Komoto, J. / Yamada, T. / Konishi, K. / Ogawa, H. / Gomi, T. / Fujioka, M. / Takusagawa, F.
History
DepositionDec 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
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)131,67312
Polymers129,8434
Non-polymers1,8308
Water5,206289
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.050, 117.010, 137.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Glycine N-methyltransferase / / Folate-binding protein / GNMT


Mass: 32460.830 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GNMT / Organ: liver / Production host: Escherichia coli (E. coli) / References: UniProt: P13255, glycine N-methyltransferase
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 3400, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mMSAM1reservoir
2100 mMsodium citrate1reservoirpH5.6
3100 mMammonium acetate1reservoir
450 mM1reservoirNaCl
510 %(w/v)PEG34001reservoir
620 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 10, 2002 / Details: Confocal optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→10 Å / Num. obs: 37008 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 5
Reflection shellResolution: 2.8→3 Å / % possible all: 81
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 36870 / % possible obs: 99 % / Num. measured all: 195411
Reflection shell
*PLUS
Lowest resolution: 2.9 Å / % possible obs: 97 % / Rmerge(I) obs: 0.258

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→10 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.278 3200 RANDOM
Rwork0.203 --
all0.22 36870 -
obs0.204 32780 -
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9140 0 124 289 9553
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg1.49
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
Refinement
*PLUS
Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more