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- PDB-5cic: Complex of yeast cytochrome c peroxidase (W191G) bound to 3-amino... -

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Basic information

Entry
Database: PDB / ID: 5cic
TitleComplex of yeast cytochrome c peroxidase (W191G) bound to 3-aminobenzotrifluoride with iso-1 cytochrome c
Components
  • Cytochrome c iso-1
  • Cytochrome c peroxidase, mitochondrial
KeywordsELECTRON TRANSPORT/OXIDOREDUCTASE / electron transfer / heme proteins / electron hopping / multi-step tunneling / photochemistry / ELECTRON TRANSPORT-OXIDOREDUCTASE complex
Function / homology
Function and homology information


Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / response to reactive oxygen species ...Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Cytochrome c-like domain / Peroxidase; domain 1 / Cytochrome Bc1 Complex; Chain D, domain 2 ...Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Cytochrome c-like domain / Peroxidase; domain 1 / Cytochrome Bc1 Complex; Chain D, domain 2 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
3-(trifluoromethyl)aniline / HEME C / Cytochrome c isoform 1 / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsCrane, B.R. / Payne, T.M.
CitationJournal: Biochemistry / Year: 2016
Title: Constraints on the Radical Cation Center of Cytochrome c Peroxidase for Electron Transfer from Cytochrome c.
Authors: Payne, T.M. / Yee, E.F. / Dzikovski, B. / Crane, B.R.
History
DepositionJul 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Oct 17, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn / struct_site
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_host_org_scientific_name ..._citation.journal_id_CSD / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_struct_oper_list.symmetry_operation / _struct_site.details
Revision 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c peroxidase, mitochondrial
B: Cytochrome c iso-1
C: Cytochrome c peroxidase, mitochondrial
D: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,73610
Polymers90,9404
Non-polymers2,7966
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-104 kcal/mol
Surface area34060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.257, 117.531, 88.446
Angle α, β, γ (deg.)90.000, 104.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome c peroxidase, mitochondrial / / CCP


Mass: 33396.102 Da / Num. of mol.: 2 / Mutation: W191G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CCP1, CCP, CPO, YKR066C / Plasmid: ppSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Protein Cytochrome c iso-1


Mass: 12073.835 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Plasmid: PBTR-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00044
#3: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-51R / 3-(trifluoromethyl)aniline / 3-(Trifluoromethyl)aniline


Mass: 161.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6F3N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.51 Å3/Da / Density % sol: 50.91 % / Description: plates
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl / PH range: 4.8-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 51366 / % possible obs: 98.7 % / Redundancy: 7 % / Net I/σ(I): 14.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.103→42.839 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 2003 3.9 %
Rwork0.1924 49360 -
obs0.1938 51363 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.41 Å2 / Biso mean: 45.285 Å2 / Biso min: 22.57 Å2
Refinement stepCycle: final / Resolution: 2.103→42.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6416 0 194 466 7076
Biso mean--38.74 45.71 -
Num. residues----804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056814
X-RAY DIFFRACTIONf_angle_d0.9179248
X-RAY DIFFRACTIONf_chiral_restr0.03902
X-RAY DIFFRACTIONf_plane_restr0.0041198
X-RAY DIFFRACTIONf_dihedral_angle_d13.512474
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.103-2.15520.29171260.24823092321886
2.1552-2.21350.32121430.236935393682100
2.2135-2.27860.28071470.236135513698100
2.2786-2.35220.29191430.237935543697100
2.3522-2.43620.23961470.21935433690100
2.4362-2.53380.29221460.221235923738100
2.5338-2.64910.24851450.217235363681100
2.6491-2.78870.2281380.211235813719100
2.7887-2.96340.25161420.215135723714100
2.9634-3.19210.24431410.210635653706100
3.1921-3.51320.22831440.200135773721100
3.5132-4.02130.21311480.171335613709100
4.0213-5.06510.19481460.15253563370999
5.0651-42.84810.18721470.17013534368197

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