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- PDB-6k9i: High-resolution three-dimensional structure of horse heart cytoch... -

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Basic information

Entry
Database: PDB / ID: 6k9i
TitleHigh-resolution three-dimensional structure of horse heart cytochrome C at room temperature
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


cytochrome c-heme linkage / cytochrome complex / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / apoptotic signaling pathway / mitochondrial intermembrane space / electron transfer activity / heme binding / lipid binding / metal ion binding ...cytochrome c-heme linkage / cytochrome complex / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / apoptotic signaling pathway / mitochondrial intermembrane space / electron transfer activity / heme binding / lipid binding / metal ion binding / identical protein 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: 1.8 Å
AuthorsSugawara, Y. / Endo, S.
CitationJournal: To Be Published
Title: High-resolution three-dimensional structure of horse heart cytochrome C
Authors: Fujita, T. / Yamamura, S. / Endo, S. / Sugawara, Y.
History
DepositionJun 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3702
Polymers11,7521
Non-polymers6191
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-24 kcal/mol
Surface area6050 Å2
Unit cell
Length a, b, c (Å)58.395, 58.395, 41.909
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) / References: UniProt: P00004
#2: Chemical ChemComp-HEC / HEME C


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


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 1.0-1.5M sodium chloride, 2.7-3.2M ammonium sulfate, 0.1M sodium phosphate
Temp details: ROOM TEMERATURE

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: ROOM TEMERATURE / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→23.9569 Å / Num. obs: 13227 / % possible obs: 99.9 % / Redundancy: 3.48 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.6
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.347 / Num. unique obs: 1292 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HRC

1hrc


Resolution: 1.8→19.72 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.784 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.097 / ESU R Free: 0.098 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1987 626 4.7 %RANDOM SELECTON
Rwork0.1663 ---
obs0.1678 12588 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.311 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 43 34 903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013900
X-RAY DIFFRACTIONr_bond_other_d0.0020.018852
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.7621213
X-RAY DIFFRACTIONr_angle_other_deg1.4491.6441989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7195105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0324.59537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82215173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.884152
X-RAY DIFFRACTIONr_chiral_restr0.0810.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02988
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02179
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8253.298417
X-RAY DIFFRACTIONr_mcbond_other2.8173.284416
X-RAY DIFFRACTIONr_mcangle_it3.8484.927520
X-RAY DIFFRACTIONr_mcangle_other3.8464.942521
X-RAY DIFFRACTIONr_scbond_it5.2573.932483
X-RAY DIFFRACTIONr_scbond_other5.2663.937481
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2725.525692
X-RAY DIFFRACTIONr_long_range_B_refined9.73336.6381018
X-RAY DIFFRACTIONr_long_range_B_other9.73136.6321018
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 57 -
Rwork0.286 905 -
obs--99.9 %

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