[English] 日本語
Yorodumi
- PDB-9rk3: Soluble domain of kustd1480, a Rieske iron-sulfur cluster protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rk3
TitleSoluble domain of kustd1480, a Rieske iron-sulfur cluster protein from Kuenenia stuttgartiensis
ComponentsSimilar to Rieske 2Fe-2S iron sulfur protein (Cytochrome b6-F complex)
KeywordsELECTRON TRANSPORT / Rieske / anammox / anaerobic ammonium oxidation / ensemble refinement
Function / homology
Function and homology information


plastoquinol-plastocyanin reductase / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding / membrane
Similarity search - Function
Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Similar to Rieske 2Fe-2S iron sulfur protein (Cytochrome b6-F complex)
Similarity search - Component
Biological speciesCandidatus Kuenenia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHauser, D. / Barends, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
Citation
Journal: Proteins / Year: 2025
Title: Rieske Iron-Sulfur Cluster Proteins From an Anaerobic Ammonium Oxidizer Suggest Unusual Energetics in Their Parent Rieske/Cytochrome b Complexes.
Authors: Hauser, D. / Sode, M. / Andreeva, E.A. / Parey, K. / Barends, T.R.M.
#1: Journal: Proteins / Year: 2022
Title: Dynamics in an unusual acyl carrier protein from a ladderane lipid-synthesizing organism
Authors: Dietl, A. / Barends, T.R.M.
History
DepositionJun 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Similar to Rieske 2Fe-2S iron sulfur protein (Cytochrome b6-F complex)
D: Similar to Rieske 2Fe-2S iron sulfur protein (Cytochrome b6-F complex)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6714
Polymers26,3202
Non-polymers3522
Water45025
1
A: Similar to Rieske 2Fe-2S iron sulfur protein (Cytochrome b6-F complex)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3362
Polymers13,1601
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Similar to Rieske 2Fe-2S iron sulfur protein (Cytochrome b6-F complex)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3362
Polymers13,1601
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.200, 76.150, 79.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Number of models8

-
Components

#1: Protein Similar to Rieske 2Fe-2S iron sulfur protein (Cytochrome b6-F complex) / Ubiquinol-cytochrome C reductase iron-sulfur subunit


Mass: 13159.925 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Kuenenia sp. (bacteria) / Gene: petC, KsCSTR_10330, KSMBR1_1275, kustd1480 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1PYR8, plastoquinol-plastocyanin reductase
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M CHES pH 9.5, 17% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Jan 1, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 25291 / % possible obs: 0.998 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.2
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 1871 / CC1/2: 0.909

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→39.51 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.94
RfactorNum. reflection% reflection
Rfree0.2761 476 4.98 %
Rwork0.2205 --
obs0.2232 9560 93.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 8 25 1889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.019
X-RAY DIFFRACTIONf_angle_d1.526
X-RAY DIFFRACTIONf_dihedral_angle_d21.77
X-RAY DIFFRACTIONf_chiral_restr0.068
X-RAY DIFFRACTIONf_plane_restr0.018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.860.3111720.26062998X-RAY DIFFRACTION95
2.86-3.610.27981490.23593030X-RAY DIFFRACTION95
3.61-39.510.25981550.19873056X-RAY DIFFRACTION91

+
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