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- PDB-7zs0: Diheme cytochrome c Kustd1711 from Kuenenia stuttgartiensis -

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Basic information

Entry
Database: PDB / ID: 7zs0
TitleDiheme cytochrome c Kustd1711 from Kuenenia stuttgartiensis
ComponentsHypothetical (Diheme) protein
KeywordsELECTRON TRANSPORT / anaerobic ammonium oxidation
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding / membrane
Similarity search - Function
Haem-binding domain, putative / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Hypothetical (Diheme) protein
Similarity search - Component
Biological speciesCandidatus Kuenenia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsAkram, M. / Barends, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Redox potential tuning by calcium ions in a novel c-type cytochrome from an anammox organism.
Authors: Akram, M. / Hauser, D. / Dietl, A. / Steigleder, M. / Ullmann, G.M. / Barends, T.R.M.
History
DepositionMay 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.year
Revision 1.3Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical (Diheme) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7457
Polymers34,2951
Non-polymers1,4496
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-82 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.920, 92.290, 54.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Hypothetical (Diheme) protein / Putative (Diheme) protein


Mass: 34295.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Kuenenia (bacteria) / Gene: KsCSTR_07890, KSMBR1_1466, kustd1711 / Production host: Shewanella oneidensis MR-1 (bacteria) / References: UniProt: Q1PZE6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M calcium acetate, 0.1 M imidazole/HCl pH 8.0 and 20% PEG 1K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.71603 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.71603 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 58099 / % possible obs: 95.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 26.22 Å2 / Rpim(I) all: 0.049 / Net I/σ(I): 20.3
Reflection shellResolution: 1.75→1.8 Å / Num. unique obs: 2755 / Rpim(I) all: 0.626

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→47.22 Å / SU ML: 0.2025 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9764 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.196 3760 6.47 %
Rwork0.1691 54339 -
obs0.1709 58099 95.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.16 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 95 256 2484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862276
X-RAY DIFFRACTIONf_angle_d0.95543106
X-RAY DIFFRACTIONf_chiral_restr0.0558333
X-RAY DIFFRACTIONf_plane_restr0.0054394
X-RAY DIFFRACTIONf_dihedral_angle_d6.47011347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.3456710.35931072X-RAY DIFFRACTION49.7
1.78-1.80.39291070.3191483X-RAY DIFFRACTION70.98
1.8-1.820.31861150.27951658X-RAY DIFFRACTION78.42
1.82-1.850.32041260.24991792X-RAY DIFFRACTION85.43
1.85-1.880.29881340.23431979X-RAY DIFFRACTION91.91
1.88-1.910.29661400.2042051X-RAY DIFFRACTION97.33
1.91-1.940.2381450.17812072X-RAY DIFFRACTION100
1.94-1.970.21041490.17532119X-RAY DIFFRACTION100
1.97-2.010.19661430.17092086X-RAY DIFFRACTION100
2.01-2.050.21951460.17132110X-RAY DIFFRACTION100
2.05-2.090.21781430.1692103X-RAY DIFFRACTION99.78
2.09-2.130.22991410.16452145X-RAY DIFFRACTION100
2.13-2.180.19321400.16552118X-RAY DIFFRACTION100
2.18-2.240.19541480.16722116X-RAY DIFFRACTION100
2.24-2.30.21051520.16422117X-RAY DIFFRACTION100
2.3-2.370.20241420.16782096X-RAY DIFFRACTION100
2.37-2.440.19981460.1662100X-RAY DIFFRACTION100
2.44-2.530.16951460.16682111X-RAY DIFFRACTION100
2.53-2.630.19981510.16722122X-RAY DIFFRACTION100
2.63-2.750.20261460.17192127X-RAY DIFFRACTION100
2.75-2.90.23581450.17112090X-RAY DIFFRACTION100
2.9-3.080.17541480.16222129X-RAY DIFFRACTION100
3.08-3.310.16641450.16212107X-RAY DIFFRACTION100
3.31-3.650.16071460.16082112X-RAY DIFFRACTION100
3.65-4.180.15371470.1522093X-RAY DIFFRACTION100
4.18-5.260.18221490.15092111X-RAY DIFFRACTION100
5.26-47.220.21061490.17632120X-RAY DIFFRACTION99.96

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