[English] 日本語
Yorodumi
- PDB-2aov: Histamine Methyltransferase Complexed with the Antifolate Drug Me... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2aov
TitleHistamine Methyltransferase Complexed with the Antifolate Drug Metoprine
ComponentsHistamine N-methyltransferase
KeywordsTRANSFERASE / CLASSIC METHYLTRANSFERASE FOLD / PROTEIN-DRUG COMPLEX
Function / homology
Function and homology information


histamine N-methyltransferase / histamine catabolic process / histamine N-methyltransferase activity / histamine metabolic process / Histidine catabolism / L-histidine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / respiratory gaseous exchange by respiratory system / methylation / centrosome ...histamine N-methyltransferase / histamine catabolic process / histamine N-methyltransferase activity / histamine metabolic process / Histidine catabolism / L-histidine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / respiratory gaseous exchange by respiratory system / methylation / centrosome / extracellular exosome / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Histamine N-methyltransferase-like / Histamine N-methyltransferase (EC 2.1.1.8) family profile. / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-(DIMETHYLAMINO)BUTYL IMIDOTHIOCARBAMATE / Chem-C2M / Histamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsHorton, J.R. / Sawada, K. / Nishibori, M. / Cheng, X.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Structural basis for inhibition of histamine N-methyltransferase by diverse drugs
Authors: Horton, J.R. / Sawada, K. / Nishibori, M. / Cheng, X.
#1: Journal: Structure / Year: 2001
Title: Polymorphic Forms of Human Histamine Methyltransferase: Structural, Thermal, and Kinetic Comparisons
Authors: Horton, J.R. / Sawada, K. / Nishibori, M. / Zhang, X. / Cheng, X.
History
DepositionAug 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: Histamine N-methyltransferase
B: Histamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5556
Polymers66,6662
Non-polymers8894
Water1,63991
1
A: Histamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7773
Polymers33,3331
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7773
Polymers33,3331
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.89, 132.89, 65.05
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein Histamine N-methyltransferase / HMT


Mass: 33333.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNMT / Plasmid: PGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: P50135, histamine N-methyltransferase
#2: Chemical ChemComp-4DI / 4-(DIMETHYLAMINO)BUTYL IMIDOTHIOCARBAMATE / SKF-91488 / 4-(-DIMETHYLAMINO)BUTYL ESTER 4(-N,N-DIMETHYLAMINO)BUTYLISOTHIOUREA


Mass: 175.295 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17N3S
#3: Chemical ChemComp-C2M / 5-(3,4-DICHLOROPHENYL)-6-METHYLPYRIMIDINE-2,4-DIAMINE / METOPRINE / METHODICHLOROPHEN


Mass: 269.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10Cl2N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 6000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 19, 2000
RadiationMonochromator: SI(111) DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.48→28 Å / Num. all: 21368 / Num. obs: 21368 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 14.8
Reflection shellResolution: 2.48→2.52 Å / Rmerge(I) obs: 0.191 / Num. unique all: 1575 / % possible all: 87.7

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1JQD

1jqd


Resolution: 2.48→28 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.254 3460 RANDOM
Rwork0.211 --
all0.211 21368 -
obs0.216 21368 -
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å22.21 Å20 Å2
2---1.26 Å20 Å2
3---2.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-28 Å
Luzzati sigma a0.31 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.48→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 56 91 4676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1.6
LS refinement shellResolution: 2.48→2.52 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection
Rfree0.308 148
Rwork0.254 -
obs-1575

+
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