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- PDB-4p4q: Complex of yeast cytochrome c peroxidase (W191F) with iso-1 cytoc... -

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Basic information

Entry
Database: PDB / ID: 4p4q
TitleComplex of yeast cytochrome c peroxidase (W191F) with iso-1 cytochrome c
Components
  • Cytochrome c iso-1
  • Cytochrome c peroxidase, mitochondrial
KeywordsELECTRON TRANSPORT / electron transfer / heme proteins / electron hopping / photochemistry
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
PROTOPORPHYRIN IX CONTAINING FE / 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.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-0749997 United States
CitationJournal: to be published
Title: Chemical constraints on the radical cation center of cytochrome c peroxidase for long-range electron transfer
Authors: Crane, B.R. / Yee, E.
History
DepositionMar 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)92,4318
Polymers89,9654
Non-polymers2,4664
Water7,819434
1
A: Cytochrome c peroxidase, mitochondrial
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2154
Polymers44,9822
Non-polymers1,2332
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)46,2154
Polymers44,9822
Non-polymers1,2332
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 (brewer's 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 / Fragment: UNP residues 7-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.41 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: Mar 13, 2013 / Details: Rh coated Si mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2→43.432 Å / Num. obs: 51802 / % possible obs: 91.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.83 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 6.45
Reflection shellResolution: 2→2.03 Å / Redundancy: 3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.81 / % possible all: 82.5

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Processing

Software
NameVersionClassification
PHASERphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementResolution: 2.01→40 Å / FOM work R set: 0.7598 / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2776 1984 3.84 %
Rwork0.2157 49720 -
obs0.2181 51704 91.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.29 Å2 / Biso mean: 31.85 Å2 / Biso min: 8.08 Å2
Refinement stepCycle: final / Resolution: 2.01→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6346 0 172 434 6952
Biso mean--22.59 30.44 -
Num. residues----794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086712
X-RAY DIFFRACTIONf_angle_d1.1749122
X-RAY DIFFRACTIONf_chiral_restr0.076892
X-RAY DIFFRACTIONf_plane_restr0.0061182
X-RAY DIFFRACTIONf_dihedral_angle_d14.6962444
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 (%)
2.01-2.06010.37821260.23673079320579
2.0601-2.11580.33451390.23243520365990
2.1158-2.17810.31881400.24143519365991
2.1781-2.24840.37061350.28893426356188
2.2484-2.32870.34031400.27433417355789
2.3287-2.4220.32091380.23863521365991
2.422-2.53220.29091410.22513535367691
2.5322-2.66570.31271390.22413557369691
2.6657-2.83260.31971440.22813571371592
2.8326-3.05130.29591460.22723628377494
3.0513-3.35830.30371530.22283761391496
3.3583-3.8440.25591480.20043774392297
3.844-4.8420.2141510.17923707385895
4.842-43.44220.21511440.19463705384993
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)
12.3657-0.75530.25992.42310.53182.41680.14850.21560.2185-0.2516-0.0987-0.0152-0.1791-0.1352-0.06540.1612-0.00270.00540.17610.00380.167723.9711-12.3143114.8612
20.8606-0.0987-0.321.286-0.02731.95540.0199-0.03790.00910.12240.0534-0.08390.0126-0.0013-0.06830.1946-0.019-0.02580.1893-0.02570.155527.1965-20.0145126.6778
31.61-0.4986-1.91170.23531.01964.4541-0.05240.3474-0.0191-0.1274-0.35070.4085-0.444-0.75130.39450.15470.0602-0.00060.327-0.04940.293912.6236-15.3083113.3844
40.77340.81360.33661.4177-0.44576.5027-0.17860.01340.4015-0.02540.0535-0.3194-0.28050.83210.14420.236-0.00090.0090.4279-0.17960.575246.1875-29.3874105.4741
51.56382.0782-0.1392.89920.6024.56650.4237-0.0535-0.08420.3868-0.2037-0.2215-0.2710.4986-0.06960.50120.1129-0.09450.2737-0.08060.391144.397-40.0483111.6581
61.2007-0.4206-0.58810.5908-0.61291.8005-0.16580.0502-0.68190.4896-0.0974-0.08540.9940.13230.15840.68670.1385-0.06480.2041-0.06920.501138.9321-47.2242108.2665
74.1284-0.21212.15414.33851.65152.84870.03510.0345-0.4772-0.05410.12460.4090.3555-0.2454-0.07430.5937-0.28130.03650.36280.00240.657126.4163-47.9846106.3239
82.84380.47540.11940.09390.0360.0215-0.31780.55680.07390.11080.1544-0.16620.5270.1690.24260.23780.03330.02140.3615-0.08230.443433.1716-45.460297.7431
96.14790.8982-0.2964.9758-1.06444.12790.30880.2220.1275-0.13740.1619-0.26030.15440.0819-0.48490.34160.03060.01480.1961-0.07980.211931.8411-36.199799.5049
102.7999-0.212-0.14530.1883-0.8974.77570.18780.036-0.1554-0.1123-0.03770.10910.1589-0.072-0.23410.3348-0.02820.0280.1388-0.03350.227630.6088-33.9493106.4423
115.8921-0.21530.95794.2812-1.4735.63750.18140.4569-0.268-0.6766-0.159-0.7997-0.03560.4809-0.03370.29350.03710.12940.5041-0.11570.419144.6279-34.044999.3739
122.28360.5409-0.44862.24670.3232.6177-0.0244-0.3163-0.07890.2758-0.05420.06310.1996-0.05540.01920.14180.00670.01870.13640.0260.147824.1381-23.519884.0796
130.86730.3751-0.03822.07910.00291.91260.0669-0.0312-0.0785-0.043-0.04470.02070.1046-0.0804-0.01010.1124-0.0062-0.0140.1613-0.00120.142226.6569-22.970273.9143
141.1499-0.13760.02351.9422-0.34052.1046-0.02940.18730.1838-0.01290.0686-0.1013-0.3074-0.09-0.04340.17360.0160.00160.1492-0.02670.139330.0166-6.597167.5553
150.3796-0.40830.11680.66340.69293.17150.0496-0.26010.04550.1126-0.18820.05740.0848-0.57490.17760.1695-0.05020.04970.3538-0.00260.227612.4688-20.263384.8068
162.64721.2774-1.69453.2447-1.23091.14940.1761-0.73820.23340.1694-0.2626-0.5475-0.66761.0079-0.11150.6547-0.33830.05520.6803-0.17040.362645.24260.973787.6148
172.1012-0.76421.35842.76151.15271.9688-0.19010.00360.2405-0.3580.02-0.0807-0.6736-0.0060.29580.9794-0.3450.11370.6846-0.27030.441639.565712.687194.1267
181.1821-0.9141-1.17330.95681.64253.32310.0559-0.05850.2576-0.1409-0.08650.1-0.4998-0.2031-0.09271.25020.07650.48060.5016-0.18280.666230.927812.633687.4134
192.99550.51550.78583.08530.40350.2297-0.4757-0.59410.60790.387-0.0111-0.1577-0.86870.1010.42980.988-0.26750.0820.6411-0.19820.458935.54.530499.1593
208.6198-0.16810.37436.2341-0.37680.03830.4603-0.44690.58910.45990.00450.2466-0.6347-0.2042-0.29890.6244-0.03520.20640.4282-0.06460.417927.45830.425194.5676
212.8870.51840.90642.0258-0.8683.26580.3502-0.66110.34030.296-0.2502-0.0233-0.88580.85450.01260.5173-0.18250.09410.5905-0.17410.301939.8021-1.553795.0127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 54 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 271 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 272 through 294 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 13 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 14 through 23 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 48 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 54 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 55 through 60 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 61 through 74 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 75 through 87 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 88 through 103 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 54 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 55 through 200 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 201 through 271 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 272 through 294 )C0
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 33 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 34 through 43 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 44 through 55 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 56 through 69 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 70 through 74 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 75 through 103 )D0

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