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- PDB-3cp5: Cytochrome c from rhodothermus marinus -

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Basic information

Entry
Database: PDB / ID: 3cp5
TitleCytochrome c from rhodothermus marinus
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / Cytochrome c / Electron transfer protein
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c
Similarity search - Component
Biological speciesRhodothermus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.24 Å
AuthorsStelter, M. / Melo, A. / Saraiva, L. / Teixeira, M. / Archer, M.
CitationJournal: Biochemistry / Year: 2008
Title: A novel type of monoheme cytochrome c: biochemical and structural characterization at 1.23 A resolution of rhodothermus marinus cytochrome c
Authors: Stelter, M. / Melo, A.M. / Pereira, M.M. / Gomes, C.M. / Hreggvidsson, G.O. / Hjorleifsdottir, S. / Saraiva, L.M. / Teixeira, M. / Archer, M.
History
DepositionMar 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5493
Polymers13,8351
Non-polymers7152
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.592, 32.644, 42.064
Angle α, β, γ (deg.)90.00, 94.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome c /


Mass: 13834.729 Da / Num. of mol.: 1 / Fragment: UNP residues 29-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodothermus marinus (bacteria) / Gene: cytC / Production host: Escherichia coli (E. coli) / References: UniProt: B3FQS5
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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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: 1.96 Å3/Da / Density % sol: 37.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2.2
Details: 30% PEG8K, 0.2M ammonium sulfate, 8% hexanediol, 50mM sodium citrate, pH2.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC / Detector: CCD / Date: Sep 24, 2006
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.23→42.41 Å / Num. all: 30888 / Num. obs: 29745 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.6
Reflection shellResolution: 1.23→1.3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 75.9

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
MxCuBEdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.24→10 Å / Num. parameters: 10515 / Num. restraintsaints: 12788 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: RESTRAINTS ON PROSTHETIC GROUPS
Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1744 1489 5.02 %RANDOM
obs0.1299 29669 91.8 %-
all-29669 --
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 885 / Occupancy sum non hydrogen: 1094.5
Refinement stepCycle: LAST / Resolution: 1.24→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 48 168 1167
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0.01
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.029
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.064
X-RAY DIFFRACTIONs_approx_iso_adps0.09

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