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- PDB-5cih: Complex of yeast cytochrome c peroxidase (W191Y) with iso-1 cytoc... -

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Basic information

Entry
Database: PDB / ID: 5cih
TitleComplex of yeast cytochrome c peroxidase (W191Y) 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: 2.6 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 1.3Jul 19, 2017Group: Database references / Derived calculations / Structure summary
Category: citation / pdbx_struct_oper_list / struct
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _struct.title
Revision 2.0Mar 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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 / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_ref_seq_dif / 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 / _entity.pdbx_mutation / _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_type.id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Nov 6, 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)92,4718
Polymers89,9974
Non-polymers2,4744
Water72140
1
A: Cytochrome c peroxidase, mitochondrial
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2354
Polymers44,9982
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)46,2354
Polymers44,9982
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.451, 114.219, 88.258
Angle α, β, γ (deg.)90.000, 104.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome c peroxidase, mitochondrial / CCP


Mass: 33502.223 Da / Num. of mol.: 2 / Fragment: UNP residues 68-361 / Mutation: T53I, D152G, W191Y
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: 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 (E. coli) / 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.: 40 / 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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 298 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 4 / Detector: CCD / Date: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 28703 / % possible obs: 76.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.088 / Rrim(I) all: 0.157 / Χ2: 1.152 / Net I/av σ(I): 7.638 / Net I/σ(I): 7.1 / Num. measured all: 88500
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.33-2.371.80.5662450.2870.4870.751.47513
2.37-2.411.90.6076110.520.4950.7861.39632.6
2.41-2.4620.8126820.470.6541.21236.8
2.46-2.512.10.8278180.4360.6561.25543.4
2.51-2.562.30.8749100.4010.6781.19948.4
2.56-2.622.50.63110030.6230.4750.7931.27453.8
2.62-2.692.60.54611710.7780.40.6791.14961.5
2.69-2.762.60.60913020.710.4350.7511.16670.5
2.76-2.842.80.61515120.7480.4350.7561.13179.5
2.84-2.942.90.53116410.8440.3630.6451.19988.4
2.94-3.043.10.5718760.8280.3840.6891.01398.5
3.04-3.163.30.42918500.9320.2780.5120.96599.8
3.16-3.313.40.33418820.9320.2130.3970.96499.7
3.31-3.483.40.23218730.960.1480.2760.98699.9
3.48-3.73.40.17718760.9660.1120.211.0599.8
3.7-3.983.40.13918820.9750.0880.1651.10699.8
3.98-4.383.40.11918840.9840.0760.1411.3899.3
4.38-5.023.40.09818780.9850.0630.1171.46599.3
5.02-6.323.60.08818910.9880.0550.1041.18799.4
6.32-503.60.0619160.9950.0370.0711.21299.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.6→35.359 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 35.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3096 1498 6.96 %
Rwork0.2232 20035 -
obs0.2289 21533 80.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 324.15 Å2 / Biso mean: 70.5858 Å2 / Biso min: 13.16 Å2
Refinement stepCycle: final / Resolution: 2.6→35.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6348 0 172 40 6560
Biso mean--64.28 55.38 -
Num. residues----794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036724
X-RAY DIFFRACTIONf_angle_d0.7139126
X-RAY DIFFRACTIONf_chiral_restr0.024892
X-RAY DIFFRACTIONf_plane_restr0.0031182
X-RAY DIFFRACTIONf_dihedral_angle_d13.3062446
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.68390.4395810.2881096117748
2.6839-2.77980.3792900.30031228131855
2.7798-2.89110.39811100.30591401151162
2.8911-3.02260.39121250.30891662178773
3.0226-3.18180.39031390.29761806194581
3.1818-3.3810.35491500.27761964211487
3.381-3.64190.32251540.2362089224392
3.6419-4.00790.29881640.22092200236497
4.0079-4.58680.28771510.18622117226892
4.5868-5.77480.27831650.19792181234695
5.7748-35.3620.25021690.18052291246099
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)
13.585-0.43610.61482.09220.16843.44510.09310.0609-0.1408-0.03610.00380.07270.1491-0.0807-0.06770.1873-0.05610.01930.3402-0.00750.2342-16.182521.7259-4.1854
24.8737-0.12751.97912.70012.41493.2076-0.12-0.16810.5234-0.57130.06550.4477-0.8952-0.21190.15130.6971-0.0809-0.10880.62740.20710.5858-35.131741.8846-19.0573
30.82350.0636-0.62441.3298-0.58072.39320.27030.34090.82120.32650.08070.4929-0.2036-0.3135-0.331.1524-0.3142-0.06280.78120.18211.5075-23.348251.7652-22.5812
43.98730.65771.14963.5116-0.42593.7361-0.07790.73380.4174-0.96520.04440.60570.1653-0.24290.01890.6311-0.151-0.11850.76870.2430.5418-27.675738.3503-26.2847
53.41371.06240.80461.55521.0653.75210.10720.0018-0.01580.04660.0617-0.05860.14230.4349-0.13540.25060.08290.01010.39310.03170.2295-16.662222.0025-52.977
61.9716-1.01951.02033.61281.10151.3805-0.1399-0.0143-0.12230.1884-0.05630.6710.32290.20390.11710.51390.1128-0.02661.3582-0.15740.491-37.723310.2378-35.5124
72.2909-0.7705-0.05681.9374-0.44911.8482-0.4519-0.1643-0.97010.2873-0.26020.91090.6374-0.44280.6451.1421-0.3368-0.14550.74050.09610.8847-35.1468-2.416-43.2787
82.55380.5268-0.35872.41160.36491.90640.5412-0.8509-0.77930.3335-0.33830.25630.248-0.2804-0.19520.9976-0.0267-0.10271.07740.16030.7236-27.1012-0.6047-33.1312
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 38 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 39 through 60 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 61 through 103 )B0
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 294 )C0
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 13 )D0
7X-RAY DIFFRACTION7chain 'D' and (resid 14 through 33 )D0
8X-RAY DIFFRACTION8chain 'D' and (resid 34 through 103)D0

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