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- PDB-9fbk: Diheme cytochrome c Kustd1711 from Kuenenia stuttgartiensis, with... -

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Basic information

Entry
Database: PDB / ID: 9fbk
TitleDiheme cytochrome c Kustd1711 from Kuenenia stuttgartiensis, without glycerol cryoprotectant
ComponentsHypothetical (Diheme) protein
KeywordsELECTRON TRANSPORT / heme C / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHauser, D. / Barends, T.R.M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other government 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 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 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
Revision 1.2Feb 5, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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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)35,7338
Polymers34,2951
Non-polymers1,4377
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-95 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.600, 92.100, 55.270
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
Components on special symmetry positions
IDModelComponents
11A-786-

HOH

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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.: 5 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
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, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.887 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.887 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 34601 / % possible obs: 94.7 % / Redundancy: 2.5 % / Biso Wilson estimate: 26.49 Å2 / Rrim(I) all: 0.127 / Net I/σ(I): 5.5
Reflection shellResolution: 1.7→1.75 Å / Num. unique obs: 4955 / Rrim(I) all: 0.818

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.43 Å / SU ML: 0.2601 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.4278
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2316 2221 6.42 %
Rwork0.1939 32380 -
obs0.1963 34601 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.96 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 91 351 2576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982293
X-RAY DIFFRACTIONf_angle_d1.113136
X-RAY DIFFRACTIONf_chiral_restr0.0618337
X-RAY DIFFRACTIONf_plane_restr0.0111400
X-RAY DIFFRACTIONf_dihedral_angle_d16.8842853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.48971390.36661995X-RAY DIFFRACTION97.62
1.74-1.780.31481380.28882051X-RAY DIFFRACTION99.82
1.78-1.830.29791390.27272032X-RAY DIFFRACTION99.63
1.83-1.880.30371410.23972027X-RAY DIFFRACTION99.36
1.88-1.930.28641390.24622017X-RAY DIFFRACTION98.81
1.93-1.990.31151400.24022053X-RAY DIFFRACTION98.78
1.99-2.060.23911390.2062036X-RAY DIFFRACTION98.02
2.06-2.150.22541380.1932014X-RAY DIFFRACTION97.16
2.15-2.240.24691410.19761997X-RAY DIFFRACTION97.27
2.24-2.360.2631320.1981998X-RAY DIFFRACTION96.55
2.36-2.510.25111350.20082003X-RAY DIFFRACTION95.96
2.51-2.70.24831400.20422011X-RAY DIFFRACTION96.11
2.7-2.980.24071380.20142006X-RAY DIFFRACTION95.8
2.98-3.410.23591370.19021997X-RAY DIFFRACTION95.27
3.41-4.290.20631400.16462035X-RAY DIFFRACTION94.85
4.29-41.430.16671450.16092108X-RAY DIFFRACTION93.64

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