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- PDB-6p42: Yeast cytochrome c peroxidase (W191Y:L232H) in complex with iso-1... -

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Basic information

Entry
Database: PDB / ID: 6p42
TitleYeast cytochrome c peroxidase (W191Y:L232H) in complex with iso-1 cytochrome c
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: 2.905 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
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.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)92,5138
Polymers90,0474
Non-polymers2,4664
Water905
1
A: Cytochrome c peroxidase, mitochondrial
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2564
Polymers45,0232
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)46,2564
Polymers45,0232
Non-polymers1,2332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.926, 111.918, 88.747
Angle α, β, γ (deg.)90.000, 105.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33527.211 Da / Num. of mol.: 2 / Mutation: W191Y, L232H
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-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.: 5 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
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 18%-20%, L-proline
PH range: 5.4-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 17844 / % possible obs: 93.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.07 / Rrim(I) all: 0.178 / Χ2: 0.516 / Net I/σ(I): 2.6 / Num. measured all: 107326
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.952.90.6855360.6820.3950.7990.456.4
2.95-33.31.0116560.3270.571.170.38469.3
3-3.063.80.9127430.450.4721.0340.40676.1
3.06-3.124.20.8067910.6710.3990.9040.41185.3
3.12-3.194.70.678750.8530.3220.7470.42592.7
3.19-3.275.30.6949400.7530.320.7680.41995.5
3.27-3.355.50.6079010.8530.2750.6690.43297.9
3.35-3.445.60.4689310.9230.210.5150.44197.5
3.44-3.546.20.3929790.9390.1680.4280.47199.2
3.54-3.656.90.3649210.9490.1470.3930.47799.9
3.65-3.787.10.2849570.9640.1140.3060.50899.6
3.78-3.9470.2429410.9740.0980.2610.51899.3
3.94-4.1170.1999560.9830.080.2150.55799.8
4.11-4.336.80.1569400.9890.0640.1690.56399.6
4.33-4.66.30.149720.9870.060.1530.57698.8
4.6-4.967.20.1289420.9920.0510.1380.55199.9
4.96-5.467.20.1289490.990.0510.1380.51599.9
5.46-6.246.90.1239710.9910.050.1330.51499.9
6.24-7.866.60.0919600.9940.0380.0990.57398.6
7.86-506.80.0679830.9950.0290.0730.74799.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CIH

5cih


Resolution: 2.905→46.817 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 32.78
RfactorNum. reflection% reflection
Rfree0.2708 1604 10.02 %
Rwork0.2119 --
obs0.2179 16004 83.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.61 Å2 / Biso mean: 68.1039 Å2 / Biso min: 30.58 Å2
Refinement stepCycle: final / Resolution: 2.905→46.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6351 0 172 5 6528
Biso mean--69.55 51.36 -
Num. residues----794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9048-2.99860.4661850.349469878346
2.9986-3.10570.4198950.3533923101859
3.1057-3.23010.40871260.311122124872
3.2301-3.3770.37411350.29911249138480
3.377-3.5550.40761490.25661390153987
3.555-3.77760.29661600.22581400156092
3.7776-4.06920.25721630.20621478164195
4.0692-4.47840.26481700.18681507167796
4.4784-5.12570.2181710.17511517168897
5.1257-6.45520.25021730.20761540171398
6.4552-46.82280.19851770.16481576175398

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