[English] 日本語
Yorodumi
- PDB-8x9v: Crystal structure of Xanthomonas oryzae pv. oryzae NADH-quinone o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8x9v
TitleCrystal structure of Xanthomonas oryzae pv. oryzae NADH-quinone oxidoreductase subunits NuoE and NuoF
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Complex
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / cellular respiration / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Soluble ligand binding domain / SLBB domain / : / NADH ubiquinone oxidoreductase, F subunit / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region ...Soluble ligand binding domain / SLBB domain / : / NADH ubiquinone oxidoreductase, F subunit / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / : / NADH-quinone oxidoreductase subunit F
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsLi, L. / Ran, T. / Wang, W. / Zhang, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972326 China
CitationJournal: To Be Published
Title: NADH-quinone oxidoreductase subunits NuoE and NuoF
Authors: Li, L. / Ran, T. / Wang, W. / Zhang, F.
History
DepositionDec 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: NADH-quinone oxidoreductase subunit F
O: NADH-quinone oxidoreductase subunit E
C: NADH-quinone oxidoreductase subunit F
D: NADH-quinone oxidoreductase subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,8329
Polymers135,4764
Non-polymers1,3565
Water2,108117
1
F: NADH-quinone oxidoreductase subunit F
O: NADH-quinone oxidoreductase subunit E
hetero molecules

C: NADH-quinone oxidoreductase subunit F
D: NADH-quinone oxidoreductase subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,8329
Polymers135,4764
Non-polymers1,3565
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area13690 Å2
ΔGint-109 kcal/mol
Surface area40850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.200, 99.910, 147.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
NADH-quinone oxidoreductase subunit ... , 2 types, 4 molecules FCOD

#1: Protein NADH-quinone oxidoreductase subunit F


Mass: 48174.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Gene: nuoF / Production host: Escherichia coli (E. coli) / References: UniProt: A0A854CMD1
#2: Protein NADH-quinone oxidoreductase subunit E


Mass: 19563.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Gene: nuoE / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M1MMP2

-
Non-polymers , 4 types, 122 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5 / Details: Bis-Tris, PEG 4000, acetone

-
Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.36→29.55 Å / Num. obs: 56860 / % possible obs: 99.9 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 14.6
Reflection shellResolution: 2.36→2.42 Å / Num. unique obs: 53377 / CC1/2: 0.807

-
Processing

Software
NameVersionClassification
PHENIXv1.16refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q9C

6q9c


Resolution: 2.36→28.84 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2476 --
Rwork0.1918 --
obs-56762 99.87 %
Displacement parametersBiso mean: 54.84 Å2
Refinement stepCycle: LAST / Resolution: 2.36→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8924 0 76 117 9117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00859227
X-RAY DIFFRACTIONf_angle_d1.064612513
X-RAY DIFFRACTIONf_chiral_restr0.05641332
X-RAY DIFFRACTIONf_plane_restr0.0081612
X-RAY DIFFRACTIONf_dihedral_angle_d17.04735390

+
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