[English] 日本語
Yorodumi
- PDB-8ht2: Crystal structure of Acetylornithine aminotransferase from Coryne... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ht2
TitleCrystal structure of Acetylornithine aminotransferase from Corynebacterium glutamicum
ComponentsAcetylornithine aminotransferase
KeywordsTRANSFERASE / Acetylornithine aminotransferase / Corynebacterium glutamicum
Function / homology
Function and homology information


acetylornithine transaminase / N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / L-arginine biosynthetic process / pyridoxal phosphate binding / identical protein binding / cytoplasm
Similarity search - Function
Acetylornithine/Succinylornithine transaminase family / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Acetylornithine aminotransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKi, D. / Kim, K.-J.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Crystal Structure and Functional Characterization of Acetylornithine Aminotransferase from Corynebacterium glutamicum.
Authors: Ki, D. / Hong, H. / Kim, I.K. / Kim, K.J.
History
DepositionDec 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetylornithine aminotransferase
B: Acetylornithine aminotransferase


Theoretical massNumber of molelcules
Total (without water)84,6362
Polymers84,6362
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-43 kcal/mol
Surface area26350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.395, 176.766, 56.139
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Acetylornithine aminotransferase / ACOAT


Mass: 42318.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: argD, Cgl1397, cg1583 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59282, acetylornithine transaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.39 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1.6 M ammonium sulfate, 0.1 M sodium HEPES pH 6.5, 0.1 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 22995 / % possible obs: 97.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.038 / Rrim(I) all: 0.09 / Χ2: 2.383 / Net I/σ(I): 13.3 / Num. measured all: 111467
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.73.30.32110750.7520.190.3761.15392.6
2.7-2.743.60.310790.8590.1710.3481.28394.6
2.74-2.83.40.28411310.8670.1620.331.31295.4
2.8-2.853.60.26710890.8620.1520.3091.38493.8
2.85-2.9240.2410980.9230.1290.2741.40996.1
2.92-2.983.90.22611290.9530.1220.2581.4596.6
2.98-3.064.10.20811250.9550.1090.2371.51496.4
3.06-3.144.30.19811260.950.1010.2241.6197
3.14-3.234.60.16811410.9730.0830.1891.74398
3.23-3.3450.15511610.9740.0740.1732.47198
3.34-3.465.20.12411490.9890.0570.1372.09898.2
3.46-3.65.30.10111480.9940.0460.1122.11797.9
3.6-3.765.60.09711770.9960.0430.1062.96899.4
3.76-3.965.60.07911560.9960.0340.0862.62298.1
3.96-4.215.50.08111680.9960.0360.0894.11397.9
4.21-4.5360.06811650.9960.0290.0753.80798.4
4.53-4.995.90.06111670.9980.0260.0662.85498
4.99-5.7160.05512130.9970.0230.062.35198.5
5.71-7.1960.05112110.9980.0220.0562.3298.5
7.19-505.60.04712870.9970.0220.0523.21497.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+54 / Resolution: 2.65→32.94 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.853 / SU B: 16.62 / SU ML: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.342 / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3023 1130 4.9 %RANDOM
Rwork0.2121 ---
obs0.2165 21850 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.83 Å2 / Biso mean: 50.87 Å2 / Biso min: 22.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-0 Å2-0 Å2
2---4.67 Å20 Å2
3---5.95 Å2
Refinement stepCycle: final / Resolution: 2.65→32.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5417 0 0 22 5439
Biso mean---38.21 -
Num. residues----734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135487
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175344
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.6347449
X-RAY DIFFRACTIONr_angle_other_deg1.211.57612271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5485728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0622.481258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.85515871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6821534
X-RAY DIFFRACTIONr_chiral_restr0.0630.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021171
LS refinement shellResolution: 2.652→2.721 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 73 -
Rwork0.32 1504 -
all-1577 -
obs--92.22 %

+
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