[English] 日本語
Yorodumi
- PDB-7yra: Crystal structure of [2Fe-2S]-TtPetA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yra
TitleCrystal structure of [2Fe-2S]-TtPetA
ComponentsUbiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsELECTRON TRANSPORT / Rieske / iron-sulfur cluster / metal binding
Function / homology
Function and homology information


quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / 2 iron, 2 sulfur cluster binding / intracellular membrane-bounded organelle / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ubiquinol-cytochrome c reductase iron-sulfur subunit
Similarity search - Component
Biological speciesThermochromatium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsTsutsumi, E. / Niwa, S. / Takeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other private Japan
CitationJournal: Commun Chem / Year: 2023
Title: Structure of a putative immature form of a Rieske-type iron-sulfur protein in complex with zinc chloride.
Authors: Tsutsumi, E. / Niwa, S. / Takeda, R. / Sakamoto, N. / Okatsu, K. / Fukai, S. / Ago, H. / Nagao, S. / Sekiguchi, H. / Takeda, K.
History
DepositionAug 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquinol-cytochrome c reductase iron-sulfur subunit
B: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,94712
Polymers32,9002
Non-polymers1,04810
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area6980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.409, 51.022, 98.805
Angle α, β, γ (deg.)90.00, 93.45, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit / TtPetA


Mass: 16449.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochromatium tepidum (bacteria) / Gene: petA / Production host: Escherichia coli (E. coli) / References: UniProt: D1MZ11, quinol-cytochrome-c reductase

-
Non-polymers , 5 types, 156 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6 M AmS, 20% glycerol, 0.1 M Na-Ac pH 4.6

-
Data collection

DiffractionMean temperature: 15 K / Ambient temp details: He cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 30162 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rsym value: 0.084 / Net I/σ(I): 10.1
Reflection shellResolution: 1.79→1.9 Å / Num. unique obs: 4797 / CC1/2: 0.927 / Rsym value: 0.323

-
Processing

Software
NameVersionClassification
CNSrefinement
XDSdata reduction
PDB_EXTRACT3.27data extraction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YR9

7yr9


Resolution: 1.79→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2386 1444 4.7 %
Rwork0.2066 27972 -
obs-29416 96.3 %
Refinement stepCycle: LAST / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 47 146 2465
LS refinement shellResolution: 1.79→1.81 Å /
RfactorNum. reflection
Rfree0.2862 35
Rwork0.28 739

+
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