[English] 日本語
Yorodumi
- PDB-1gey: CRYSTAL STRUCTURE OF HISTIDINOL-PHOSPHATE AMINOTRANSFERASE COMPLE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gey
TitleCRYSTAL STRUCTURE OF HISTIDINOL-PHOSPHATE AMINOTRANSFERASE COMPLEXED WITH N-(5'-PHOSPHOPYRIDOXYL)-L-GLUTAMATE
ComponentsHISTIDINOL-PHOSPHATE AMINOTRANSFERASE
KeywordsTRANSFERASE / alpha/beta-structure / N-(5'-PHOSPHOPYRIDOXYL)-L-GLUTAMATE / PPE / complex
Function / homology
Function and homology information


histidinol-phosphate transaminase / histidinol-phosphate transaminase activity / L-histidine biosynthetic process / pyridoxal phosphate binding / identical protein binding / cytosol
Similarity search - Function
Histidinol-phosphate aminotransferase family / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Histidinol-phosphate aminotransferase family / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PPE / Histidinol-phosphate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsHaruyama, K. / Nakai, T. / Miyahara, I. / Hirotsu, K. / Mizuguchi, H. / Hayashi, H. / Kagamiyama, H.
CitationJournal: Biochemistry / Year: 2001
Title: Structures of Escherichia coli histidinol-phosphate aminotransferase and its complexes with histidinol-phosphate and N-(5'-phosphopyridoxyl)-L-glutamate: double substrate recognition of the enzyme.
Authors: Haruyama, K. / Nakai, T. / Miyahara, I. / Hirotsu, K. / Mizuguchi, H. / Hayashi, H. / Kagamiyama, H.
History
DepositionNov 30, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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_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: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7732
Polymers39,3941
Non-polymers3791
Water2,090116
1
A: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
hetero molecules

A: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5474
Polymers78,7882
Non-polymers7592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6210 Å2
ΔGint-19 kcal/mol
Surface area24590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.213, 63.732, 46.199
Angle α, β, γ (deg.)90.00, 104.25, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold.

-
Components

#1: Protein HISTIDINOL-PHOSPHATE AMINOTRANSFERASE


Mass: 39393.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HISC / Plasmid: PUC118 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P06986, histidinol-phosphate transaminase
#2: Chemical ChemComp-PPE / 4-[(1,3-DICARBOXY-PROPYLAMINO)-METHYL]-3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDINIUM / PYRIDOXYL-GLUTAMIC ACID-5'-MONOPHOSPHATE


Mass: 379.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: PEG 4000, magnesium chloride, tris, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-25 mg/mlprotein1drop
221 %(w/v)PEG40001reservoir
3200 mM1reservoirMgCl2
4100 mMTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 55982 / Num. obs: 55982 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 30.225 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.17
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.265 / Num. unique all: 1628 / % possible all: 97.4
Reflection
*PLUS
Num. obs: 16231 / Num. measured all: 55982
Reflection shell
*PLUS
% possible obs: 97.4 %

-
Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1GEW

1gew


Resolution: 2.3→8 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 818 -RANDOM
Rwork0.178 ---
all0.185 16231 --
obs0.182 16008 97.8 %-
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 25 116 2750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.316
X-RAY DIFFRACTIONx_torsion_deg23.921
X-RAY DIFFRACTIONx_torsion_impr_deg1.113
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.349 / Rfactor Rwork: 0.24

+
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