[English] 日本語
Yorodumi
- PDB-4qcj: Crystal Structure of OdhI from Corynebacterium glutamicum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qcj
TitleCrystal Structure of OdhI from Corynebacterium glutamicum
ComponentsOxoglutarate dehydrogenase inhibitor
KeywordsPROTEIN BINDING / FHA-domain / Signal transduction / ODHA
Function / homology
Function and homology information


: / : / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Oxoglutarate dehydrogenase inhibitor
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLabahn, J. / Raasch, K. / Eggeling, L. / Bocola, M. / Leitner, A. / Bott, M.
CitationJournal: J.Biotechnol. / Year: 2014
Title: Interaction of 2-oxoglutarate dehydrogenase OdhA with its inhibitor OdhI in Corynebacterium glutamicum: Mutants and a model.
Authors: Raasch, K. / Bocola, M. / Labahn, J. / Leitner, A. / Eggeling, L. / Bott, M.
History
DepositionMay 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oxoglutarate dehydrogenase inhibitor


Theoretical massNumber of molelcules
Total (without water)15,4171
Polymers15,4171
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.026, 51.229, 35.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-287-

HOH

-
Components

#1: Protein Oxoglutarate dehydrogenase inhibitor


Mass: 15417.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: cg1630, Cgl1441, odhI / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NQJ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.51 Å3/Da / Density % sol: 18.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 17% PEG 3350, 0.2 M Sodium malonate, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 13, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→51 Å / Num. all: 6688 / Num. obs: 6634 / % possible obs: 99.2 % / Observed criterion σ(F): 20894 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.11 Å / % possible all: 99.7

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.19 Å / SU ML: 0.17 / σ(F): 1.38 / Phase error: 21.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.24 639 9.67 %random
Rwork0.1734 ---
obs0.1797 6611 99.01 %-
all-6688 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms777 0 0 135 912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007791
X-RAY DIFFRACTIONf_angle_d1.0571072
X-RAY DIFFRACTIONf_dihedral_angle_d12.841294
X-RAY DIFFRACTIONf_chiral_restr0.072120
X-RAY DIFFRACTIONf_plane_restr0.004146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0003-2.15470.23951250.18321176X-RAY DIFFRACTION100
2.1547-2.37150.26951290.17381167X-RAY DIFFRACTION99
2.3715-2.71440.26341290.18371179X-RAY DIFFRACTION99
2.7144-3.41910.22031230.17971193X-RAY DIFFRACTION99
3.4191-29.1930.22891330.16161257X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 35.0905 Å / Origin y: 11.7625 Å / Origin z: 17.6888 Å
111213212223313233
T0.0545 Å20.0035 Å20.0489 Å2-0.0289 Å2-0.0203 Å2--0.0281 Å2
L0.105 °2-0.0238 °20.0238 °2-0.0675 °20.0027 °2--0.0574 °2
S0.0646 Å °0.0187 Å °-0.0584 Å °-0.0109 Å °-0.0593 Å °0.0067 Å °0.0083 Å °-0.0045 Å °0.0829 Å °
Refinement TLS groupSelection details: all

+
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