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- PDB-7o38: cytochrome C kustc0562 from Kuenenia stuttgartiensis -

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Basic information

Entry
Database: PDB / ID: 7o38
Titlecytochrome C kustc0562 from Kuenenia stuttgartiensis
ComponentsCytochrome c-552 Ks_3357
KeywordsELECTRON TRANSPORT / anaerobic ammonium oxidation / cytochrome c / redox protein
Function / homology
Function and homology information


electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class IC / : / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / IMIDAZOLE / Cytochrome c-552 Ks_3357
Similarity search - Component
Biological speciesKuenenia stuttgartiensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBock, J. / Akram, M. / Barends, T.
CitationJournal: Acs Omega / Year: 2021
Title: Specificity of Small c -Type Cytochromes in Anaerobic Ammonium Oxidation.
Authors: Akram, M. / Bock, J. / Dietl, A. / Barends, T.R.M.
History
DepositionApr 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c-552 Ks_3357
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9604
Polymers10,2371
Non-polymers7233
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-28 kcal/mol
Surface area5140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.650, 101.650, 28.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

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Components

#1: Protein Cytochrome c-552 Ks_3357 / Similar to cytochrome c-553


Mass: 10236.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kuenenia stuttgartiensis (bacteria) / Gene: petJ, kustc0562 / Production host: Shewanella oneidensis MR-1 (bacteria) / References: UniProt: Q30JB4
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M NaCl, 30% w/v PEG 8000, 0.1 M imidazole pH 8.0, 0.277 mM cyclohexylethanoyl-N-hydroxyethylglucamide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 1, 2018 / Details: KB MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→44.02 Å / Num. obs: 3395 / % possible obs: 95.8 % / Redundancy: 2.4 % / Biso Wilson estimate: 33.72 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.041 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.166 / Num. unique obs: 307 / CC1/2: 0.745 / Rsym value: 0.174

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MXY

5mxy


Resolution: 3→40 Å / SU ML: 0.3025 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.8003
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2478 342 10.09 %
Rwork0.1913 3048 -
obs0.1969 3390 95.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.21 Å2
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms646 0 49 7 702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135714
X-RAY DIFFRACTIONf_angle_d1.5733974
X-RAY DIFFRACTIONf_chiral_restr0.065393
X-RAY DIFFRACTIONf_plane_restr0.008122
X-RAY DIFFRACTIONf_dihedral_angle_d15.934496
LS refinement shellResolution: 3→3.1 Å
RfactorNum. reflection% reflection
Rfree0.2878 170 -
Rwork0.2216 1522 -
obs--97.3 %

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