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- PDB-9rk4: Soluble domain of kuste4569, a Rieske iron-sulfur cluster protein... -

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Basic information

Entry
Database: PDB / ID: 9rk4
TitleSoluble domain of kuste4569, a Rieske iron-sulfur cluster protein from Kuenenia stuttgartiensis
ComponentsSimilar to the Rieske Protein II of bc1 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 the Rieske Protein II of bc1 complex
Similarity search - Component
Biological speciesCandidatus Kuenenia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHauser, D. / Barends, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: 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.
History
DepositionJun 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Similar to the Rieske Protein II of bc1 complex
B: Similar to the Rieske Protein II of bc1 complex
C: Similar to the Rieske Protein II of bc1 complex
D: Similar to the Rieske Protein II of bc1 complex
E: Similar to the Rieske Protein II of bc1 complex
F: Similar to the Rieske Protein II of bc1 complex
G: Similar to the Rieske Protein II of bc1 complex
H: Similar to the Rieske Protein II of bc1 complex
I: Similar to the Rieske Protein II of bc1 complex
J: Similar to the Rieske Protein II of bc1 complex
K: Similar to the Rieske Protein II of bc1 complex
L: Similar to the Rieske Protein II of bc1 complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,30436
Polymers146,04112
Non-polymers3,26324
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20300 Å2
ΔGint-408 kcal/mol
Surface area58050 Å2
Unit cell
Length a, b, c (Å)103.961, 120.730, 209.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Similar to the Rieske Protein II of bc1 complex / Ubiquinol-cytochrome C reductase iron-sulfur subunit


Mass: 12170.083 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Kuenenia sp. (bacteria) / Gene: qcrB, qcrB_2, KsCSTR_29680, KSMBR1_3797, kuste4569 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1Q5P2, plastoquinol-plastocyanin reductase
#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 72.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4% (v/v) 2,2,2-trifluoroethanol, 2 M ammonium sulfate

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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: Sep 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.8→105 Å / Num. obs: 65436 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 13
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 6430 / CC1/2: 0.803

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→73.74 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2972 3289 5.04 %
Rwork0.2645 --
obs0.2661 65271 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→73.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10260 0 108 0 10368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210596
X-RAY DIFFRACTIONf_angle_d0.51514340
X-RAY DIFFRACTIONf_dihedral_angle_d12.9323960
X-RAY DIFFRACTIONf_chiral_restr0.0471608
X-RAY DIFFRACTIONf_plane_restr0.0051848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.840.491210.43572637X-RAY DIFFRACTION100
2.84-2.890.42191360.40812699X-RAY DIFFRACTION100
2.89-2.930.41571400.36972642X-RAY DIFFRACTION100
2.93-2.980.37951560.34482661X-RAY DIFFRACTION100
2.98-3.040.38931300.32872644X-RAY DIFFRACTION99
3.04-3.10.35251180.31972709X-RAY DIFFRACTION99
3.1-3.160.37081700.31312624X-RAY DIFFRACTION99
3.16-3.230.33341610.3152635X-RAY DIFFRACTION100
3.23-3.30.33371420.31122674X-RAY DIFFRACTION100
3.3-3.390.32811380.31342716X-RAY DIFFRACTION100
3.39-3.480.34461550.28652651X-RAY DIFFRACTION100
3.48-3.580.28991310.27452707X-RAY DIFFRACTION100
3.58-3.70.29821580.25632686X-RAY DIFFRACTION100
3.7-3.830.2651300.25252687X-RAY DIFFRACTION100
3.83-3.980.2761410.25632706X-RAY DIFFRACTION100
3.98-4.160.28051430.24162702X-RAY DIFFRACTION100
4.16-4.380.26991240.23272720X-RAY DIFFRACTION100
4.38-4.660.23871380.21552710X-RAY DIFFRACTION100
4.66-5.020.24041600.21722718X-RAY DIFFRACTION100
5.02-5.520.27591540.22622724X-RAY DIFFRACTION100
5.52-6.320.30681470.24952738X-RAY DIFFRACTION100
6.32-7.960.30141540.26582800X-RAY DIFFRACTION100
7.96-73.740.27251420.2412792X-RAY DIFFRACTION96

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