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- PDB-6p43: Yeast cytochrome c peroxidase in complex with iso-1 cytochrome c ... -

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Basic information

Entry
Database: PDB / ID: 6p43
TitleYeast cytochrome c peroxidase in complex with iso-1 cytochrome c (Y48K)
Components
  • Cytochrome c iso-1
  • Cytochrome c peroxidase, mitochondrial
KeywordsElectron transport/Oxidoreductase / heme proteins / electron hopping / multi-step tunneling / electron transport-oxidoreductase complex / ELECTRON TRANSPORT
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 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / 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 / Peroxidase; domain 1 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.913 Å
AuthorsYee, E.F. / Crane, B.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Tuning Radical Relay Residues by Proton Management Rescues Protein Electron Hopping.
Authors: Yee, E.F. / Dzikovski, B. / Crane, B.R.
History
DepositionMay 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,9246
Polymers79,0743
Non-polymers1,8493
Water13,043724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-72 kcal/mol
Surface area30000 Å2
Unit cell
Length a, b, c (Å)45.208, 50.890, 86.429
Angle α, β, γ (deg.)105.640, 95.020, 107.310
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 33525.258 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: 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: 12023.775 Da / Num. of mol.: 1 / Mutation: Y48K
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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 724 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium acetate, 175 mM NaCl, 5 mM n-octyl-B-D-glucoside, polyethylene glycol 3350 14%-20%
PH range: 4.6-5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 43668 / % possible obs: 81.7 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.076 / Rrim(I) all: 0.108 / Χ2: 2.427 / Net I/σ(I): 14.4 / Num. measured all: 70369
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.931.60.59222460.5670.5920.8381.36482.4
1.93-1.971.60.34222190.650.3420.4831.48483.8
1.97-2.011.60.24622410.7480.2460.3481.40283.7
2.01-2.051.60.21122250.7880.2110.2981.76583.5
2.05-2.091.60.19822760.7920.1980.282.13983.6
2.09-2.141.60.16921800.8490.1690.2391.92883.7
2.14-2.191.60.15122660.8750.1510.2141.91484.3
2.19-2.251.60.14622530.910.1460.2062.07784
2.25-2.321.60.13822210.9320.1380.1962.1384.7
2.32-2.391.60.12522820.9420.1250.1772.384
2.39-2.481.60.11222460.9580.1120.1592.50784.2
2.48-2.581.60.10422040.9660.1040.1472.66483.5
2.58-2.71.60.08722360.9730.0870.1242.93582.7
2.7-2.841.60.07721720.9780.0770.1092.7981.7
2.84-3.021.60.06721580.9840.0670.0952.92581.6
3.02-3.251.70.04821740.9890.0480.0682.5181.5
3.25-3.581.70.04421660.9910.0440.0623.24980.3
3.58-4.091.70.03820630.9930.0380.0543.38277.4
4.09-5.161.70.03819820.9920.0380.0543.40274.4
5.16-501.80.03618580.9920.0360.0513.17869.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.913→23.261 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 22.83
RfactorNum. reflection% reflection
Rfree0.2282 1886 4.56 %
Rwork0.1909 --
obs0.1927 41357 76.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.78 Å2 / Biso mean: 23.3579 Å2 / Biso min: 2.24 Å2
Refinement stepCycle: final / Resolution: 1.913→23.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5586 0 129 724 6439
Biso mean--15.68 27.87 -
Num. residues----696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9129-1.96460.30321180.25312503262162
1.9646-2.02240.25091470.22473044319178
2.0224-2.08760.28121580.22243239339781
2.0876-2.16220.27781540.21173230338483
2.1622-2.24870.22771550.19923230338582
2.2487-2.35090.25191470.21073102324978
2.3509-2.47470.23751380.20343034317277
2.4747-2.62960.2341410.19932968310976
2.6296-2.83230.2151520.19563070322277
2.8323-3.11670.20451450.19093035318078
3.1167-3.56630.21831510.17513167331880
3.5663-4.48790.19141470.15193047319477
4.4879-23.26270.21321330.17442802293571

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