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- PDB-5cid: Complex of yeast cytochrome c peroxidase (W191G) bound to o-tolui... -

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Basic information

Entry
Database: PDB / ID: 5cid
TitleComplex of yeast cytochrome c peroxidase (W191G) bound to o-toluidine 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


Release of apoptotic factors from the mitochondria / Pyroptosis / 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 ...Release of apoptotic factors from the mitochondria / Pyroptosis / 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
2-methylaniline / HEME C / Cytochrome c isoform 1 / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.763 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 12, 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 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_site
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 / _citation.journal_id_CSD / _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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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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)93,62810
Polymers90,9404
Non-polymers2,6886
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-99 kcal/mol
Surface area33800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.380, 111.906, 87.894
Angle α, β, γ (deg.)90.000, 104.330, 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 / Fragment: 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 (E. coli) / 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 (E. coli) / 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-51V / 2-methylaniline / o-Toluidine / O-Toluidine


Mass: 107.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting 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: 2.75→50 Å / Num. obs: 20376 / % possible obs: 93.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 50.57 Å2 / Rmerge(I) obs: 0.092 / Χ2: 1.019 / Net I/av σ(I): 17.182 / Net I/σ(I): 7.7 / Num. measured all: 109129
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.75-2.84.40.3887170.72165.7
2.8-2.854.40.3577510.80969.9
2.85-2.94.60.3128020.76974.7
2.9-2.964.60.3618830.7781.4
2.96-3.034.70.3139880.7888.4
3.03-3.14.90.2719770.81492.6
3.1-3.175.10.25910610.87897.5
3.17-3.265.30.24510970.87599.6
3.26-3.365.60.20710640.899100
3.36-3.465.70.15511040.969100
3.46-3.595.80.13610671.011100
3.59-3.735.70.12210951.162100
3.73-3.95.70.09810751.18100
3.9-4.115.70.08611051.206100
4.11-4.365.70.07310761.318100
4.36-4.75.70.06810931.41299.9
4.7-5.175.70.06411041.137100
5.17-5.925.70.06410881.066100
5.92-7.465.60.05511121.07299.9
7.46-505.50.04211170.90599.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.763→42.58 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 1992 9.79 %
Rwork0.2142 18349 -
obs0.2197 20341 92.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.29 Å2 / Biso mean: 70.2455 Å2 / Biso min: 23.29 Å2
Refinement stepCycle: final / Resolution: 2.763→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6416 0 188 9 6613
Biso mean--69.26 54.35 -
Num. residues----804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056808
X-RAY DIFFRACTIONf_angle_d0.8799236
X-RAY DIFFRACTIONf_chiral_restr0.031902
X-RAY DIFFRACTIONf_plane_restr0.0041198
X-RAY DIFFRACTIONf_dihedral_angle_d14.9572472
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 (%)
2.7627-2.83180.3489930.269386095360
2.8318-2.90830.35331020.2667999110173
2.9083-2.99390.32861300.2861148127882
2.9939-3.09050.39961360.27961280141690
3.0905-3.20090.34351460.28331362150897
3.2009-3.3290.35431490.279314051554100
3.329-3.48050.35261580.249414141572100
3.4805-3.66390.2731510.229413931544100
3.6639-3.89330.28251500.207213971547100
3.8933-4.19360.25071590.201214271586100
4.1936-4.61520.19941480.17614061554100
4.6152-5.2820.22181510.193414011552100
5.282-6.65070.30641570.209314231580100
6.6507-42.58490.19421620.166814341596100

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