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- PDB-6ff5: X-ray structure of bovine heart cytochrome c at high ionic strength -

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Basic information

Entry
Database: PDB / ID: 6ff5
TitleX-ray structure of bovine heart cytochrome c at high ionic strength
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / cytochrome c
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / Respiratory electron transport ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial intermembrane space / electron transfer activity / apoptotic process / heme binding / metal ion binding
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 / NITRATE ION / Cytochrome c
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsMerlino, A.
CitationJournal: Biometals / Year: 2018
Title: X-ray structure of bovine heart cytochrome c at high ionic strength.
Authors: Merlino, A.
History
DepositionJan 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.0Aug 26, 2026Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6228
Polymers11,5951
Non-polymers1,0277
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-31 kcal/mol
Surface area5940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.350, 83.350, 92.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-351-

HOH

31A-376-

HOH

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Components

#1: Protein Cytochrome c


Mass: 11595.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P62894
#2: Chemical ChemComp-HEC / HEME C


Mass: 620.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H36FeN4O4
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 3.2-3.4 M ammonium sulfate and 0.4-0.5 M NaNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.966 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.74→56.9 Å / Num. obs: 12830 / % possible obs: 99.6 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.4
Reflection shellResolution: 1.74→1.78 Å / Rmerge(I) obs: 0.8 / Num. unique obs: 3810 / CC1/2: 0.725 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B4Z

2b4z


Resolution: 1.74→56.9 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.318 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20255 638 5 %RANDOM
Rwork0.16072 ---
obs0.16289 12192 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.657 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.15 Å2-0 Å2
2---0.31 Å2-0 Å2
3---1 Å2
Refinement stepCycle: 1 / Resolution: 1.74→56.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 68 77 959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.019946
X-RAY DIFFRACTIONr_bond_other_d0.0020.02858
X-RAY DIFFRACTIONr_angle_refined_deg2.0752.0551277
X-RAY DIFFRACTIONr_angle_other_deg1.11832008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6725.26338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81615174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg34.581153
X-RAY DIFFRACTIONr_chiral_restr0.1240.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021072
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02187
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_it2.9013.32435
X-RAY DIFFRACTIONr_mcbond_other2.833.311434
X-RAY DIFFRACTIONr_mcangle_it3.7684.953549
X-RAY DIFFRACTIONr_mcangle_other3.7824.96550
X-RAY DIFFRACTIONr_scbond_it4.9013.739510
X-RAY DIFFRACTIONr_scbond_other4.8643.717483
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3465.325701
X-RAY DIFFRACTIONr_long_range_B_refined8.32738.7971117
X-RAY DIFFRACTIONr_long_range_B_other8.24738.4621107
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.739→1.784 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 45 -
Rwork0.259 892 -
obs--100 %

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