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- PDB-5cif: Complex of yeast cytochrome c peroxidase (W191F) with iso-1 cytoc... -

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Basic information

Entry
Database: PDB / ID: 5cif
TitleComplex of yeast cytochrome c peroxidase (W191F) 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 / cardiolipin binding / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / response to reactive oxygen species ...Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase / cardiolipin binding / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / 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 / Peroxidases heam-ligand binding site / Cytochrome c-like domain / Peroxidase, active site ...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 / Peroxidases heam-ligand binding site / Cytochrome c-like domain / Peroxidase, active site / Peroxidases active site signature. / Cytochrome Bc1 Complex; Chain D, domain 2 / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / 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
HEME C / Cytochrome c isoform 1 / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.01 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 2.0Oct 17, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / entity_src_gen / pdbx_nonpoly_scheme / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn
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 / _citation.journal_id_CSD / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_oper_list.symmetry_operation
Revision 3.0Mar 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
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
Revision 3.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)92,4398
Polymers89,9654
Non-polymers2,4744
Water9,620534
1
A: Cytochrome c peroxidase, mitochondrial
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2194
Polymers44,9822
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cytochrome c peroxidase, mitochondrial
D: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2194
Polymers44,9822
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.797, 113.842, 88.239
Angle α, β, γ (deg.)90.000, 105.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome c peroxidase, mitochondrial / CCP


Mass: 33486.223 Da / Num. of mol.: 2 / Fragment: UNP residues 68-361 / Mutation: W191F
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: 11496.186 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


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.41 Å3/Da / Density % sol: 49.01 %
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: Oct 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 51828 / % possible obs: 92.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.222 / Χ2: 2.295 / Net I/av σ(I): 7.347 / Net I/σ(I): 14.9 / Num. measured all: 173068
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.0330.48825161.62490.7
2.03-2.073.20.45725361.70190.7
2.07-2.113.50.43925421.8790.2
2.11-2.153.50.41825151.91991.2
2.15-2.23.30.67125432.82889.1
2.2-2.2530.36424823.73889.9
2.25-2.313.10.47225303.06389.3
2.31-2.373.40.30925292.24491.2
2.37-2.443.50.2725402.16890.1
2.44-2.523.50.26225562.3391.6
2.52-2.613.50.24125652.25890.6
2.61-2.713.40.22125652.25192.2
2.71-2.843.50.20725842.25792
2.84-2.993.40.20526342.24693.4
2.99-3.173.40.19526922.26495.7
3.17-3.423.40.18627472.13897.8
3.42-3.7630.18326962.25396
3.76-4.313.40.18327112.06996.3
4.31-5.433.40.19527012.22494.7
5.43-503.30.25126442.73691.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.01→43.432 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2675 1984 3.84 %
Rwork0.2157 --
obs0.2177 51701 91.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.12 Å2 / Biso mean: 33.6041 Å2 / Biso min: 8.27 Å2
Refinement stepCycle: final / Resolution: 2.01→43.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6346 0 172 534 7052
Biso mean--26.07 35.88 -
Num. residues----794
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.259-0.1365-0.15260.42930.25420.6930.0630.0071-0.00160.0283-0.0091-0.027-0.0332-0.0794-00.113-0.0046-0.01060.1187-0.00990.11725.4982-18.2266123.4778
20.01010.00340.02290.00480.002-0.0130.1392-0.00590.11570.13680.1607-0.125-0.11530.2341-00.21470.0015-0.04320.2557-0.0750.302545.3496-34.2254108.2691
30.0062-0.0118-0.00720.0026-0.0057-0.0023-0.01150.0113-0.15080.1792-0.0862-0.07940.22050.0378-00.49550.0998-0.08610.0045-0.04540.359138.5039-47.2049108.3961
40.01070.01210.00590.00720.01630.02270.17910.1135-0.04370.19520.13830.010.0754-0.167700.1976-0.0310.00990.1607-0.06910.23831.1988-40.7021100.1625
50.02750.02380.0004-0.00080.01860.01850.15160.166-0.0829-0.13050.0193-0.09030.08790.099200.22140.00770.06250.2075-0.08490.243638.9864-34.0034102.231
60.32390.0898-0.12340.59060.07170.56850.0414-0.0351-0.0267-0.0592-0.0498-0.031-0.0144-0.0909-00.0565-0.0061-0.00650.0927-0.00120.092325.9847-18.665374.9951
70.0040.0015-0.00210.006-0.0017-00.1025-0.04120.0469-0.05430.06140.023-0.023-0.007700.211-0.1422-0.01830.6567-0.06520.193946.887-6.676492.2197
80.0063-0.01070.00550.00710.00070.00040.0591-0.0173-0.242-0.0449-0.05260.0370.06750.1212-00.3572-0.9178-0.0006-0.3104-0.42660.103544.17445.730484.6823
9-00.01110.00450.00830.0068-0.00560.130.02670.116-0.0216-0.0299-0.0278-0.1715-0.051601.0449-0.32250.35310.1799-0.41740.500534.738912.165492.0991
10-0.0092-0.01340.04780.02760.01950.0110.3292-0.25170.02340.0644-0.0710.3751-0.36690.329100.4381-0.16610.1366-0.0115-0.6649-0.688737.2663-0.730795.8794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 294 )A0
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 23 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 24 through 49 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 50 through 74 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 75 through 103 )B0
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 294 )C0
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 13 )D0
8X-RAY DIFFRACTION8chain 'D' and (resid 14 through 33 )D0
9X-RAY DIFFRACTION9chain 'D' and (resid 34 through 60 )D0
10X-RAY DIFFRACTION10chain 'D' and (resid 61 through 103 )D0

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