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- PDB-6k9j: 0.98 A three-dimensional structure of horse heart cytochrome C at 110K -

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Basic information

Entry
Database: PDB / ID: 6k9j
Title0.98 A three-dimensional structure of horse heart cytochrome C at 110K
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process ...cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process / apoptotic process / lipid binding / heme binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Cytochrome c
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsSugawara, Y. / Endo, S.
CitationJournal: To Be Published
Title: 0.98 A three-dimensional structure of horse heart cytochrome C at 110K
Authors: Sugawara, Y. / Endo, S.
History
DepositionJun 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)12,3702
Polymers11,7521
Non-polymers6191
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-24 kcal/mol
Surface area6350 Å2
Unit cell
Length a, b, c (Å)56.887, 56.887, 42.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Cytochrome c /


Mass: 11751.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Tissue: heart / References: UniProt: P00004
#2: Chemical ChemComp-HEC / HEME C / Heme C


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


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.94 Å3/Da / Density % sol: 58.23 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 1.0-1.5M sodium chloride, 2.7-3.2M ammonium sulfate, 0.1M sodium phosphate
Temp details: ROOM EMERATURE

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 0.98→25.4 Å / Num. obs: 77173 / % possible obs: 99.1 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 26.02
Reflection shellResolution: 0.98→1.01 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 3.43 / Num. unique obs: 7715 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXL2017/1refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HRC

1hrc


Resolution: 0.98→10 Å / Cross valid method: FREE R-VALUE / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1526 3918 5.08 %Random selection
Rwork0.1307 73199 --
obs-77117 99.1 %-
Refinement stepCycle: LAST / Resolution: 0.98→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 43 217 1086
LS refinement shellResolution: 0.98→1.02 Å
RfactorNum. reflection% reflection
Rfree0.206 398 4.95 %
Rwork0.202 7640 -
obs--100 %

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