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- PDB-6p41: Yeast cytochrome c peroxidase (W191Y:L232E) in complex with iso-1... -

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Basic information

Entry
Database: PDB / ID: 6p41
TitleYeast cytochrome c peroxidase (W191Y:L232E) 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


Release of apoptotic factors from the mitochondria / Pyroptosis / 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 ...Release of apoptotic factors from the mitochondria / Pyroptosis / 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: 2.9 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)92,4638
Polymers89,9974
Non-polymers2,4664
Water0
1
A: Cytochrome c peroxidase, mitochondrial
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2314
Polymers44,9982
Non-polymers1,2332
Water0
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)46,2314
Polymers44,9982
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.803, 112.070, 88.327
Angle α, β, γ (deg.)90.000, 104.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33518.180 Da / Num. of mol.: 2 / Mutation: W191Y, L232E
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: 11480.120 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

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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: 2.37 Å3/Da / Density % sol: 48.19 %
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%
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: Jun 6, 2017
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: 18648 / % possible obs: 96.2 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.076 / Rrim(I) all: 0.191 / Χ2: 1.128 / Net I/σ(I): 3.9 / Num. measured all: 109662
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.953.51.1747370.5620.6251.3410.53476.6
2.95-33.81.457860.3730.7371.6370.46483.9
3-3.0641.3728950.4340.6951.5470.48189.1
3.06-3.1241.2348540.4710.6411.40.50591.3
3.12-3.194.40.949020.7590.4721.0570.55993.6
3.19-3.275.50.979640.6820.4391.0680.53398.5
3.27-3.355.90.8489460.8030.370.9280.54699.5
3.35-3.446.30.6679520.9080.2850.7270.61399.7
3.44-3.546.40.5759880.9060.2440.6260.69999.7
3.54-3.656.40.4889480.9140.2060.5310.748100
3.65-3.786.50.399740.9390.1640.4240.80899.7
3.78-3.946.40.3019420.9680.1280.3270.99498.8
3.94-4.1160.2639560.9640.1150.2881.13998.5
4.11-4.336.60.2079720.9860.0870.2251.36499.4
4.33-4.670.1779690.9850.0720.1911.44599.7
4.6-4.9670.169580.9840.0650.1731.56599.5
4.96-5.466.80.1449660.9880.0590.1561.38499.9
5.46-6.246.20.1239600.9890.0530.1351.44298.2
6.24-7.8670.0959870.9940.0390.1031.72899.7
7.86-506.40.0799920.9920.0350.0872.99598.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CIH

5cih


Resolution: 2.9→44.317 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.53
RfactorNum. reflection% reflection
Rfree0.2726 1837 9.98 %
Rwork0.2372 --
obs0.2409 18407 95.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.33 Å2 / Biso mean: 89.4655 Å2 / Biso min: 48.03 Å2
Refinement stepCycle: final / Resolution: 2.9→44.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6350 0 172 0 6522
Biso mean--94.83 --
Num. residues----794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026716
X-RAY DIFFRACTIONf_angle_d0.5429128
X-RAY DIFFRACTIONf_dihedral_angle_d13.0193888
X-RAY DIFFRACTIONf_chiral_restr0.037890
X-RAY DIFFRACTIONf_plane_restr0.0041184
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 (%)
2.9-2.97840.45191190.39731000111977
2.9784-3.0660.4051310.38411162129387
3.066-3.1650.3921320.32021189132190
3.165-3.27810.33741430.32281323146698
3.2781-3.40930.37621480.30311298144699
3.4093-3.56440.3611460.282313371483100
3.5644-3.75220.30581440.257713041448100
3.7522-3.98710.30761460.22471294144099
3.9871-4.29470.28871460.22141317146399
4.2947-4.72650.21791420.209213321474100
4.7265-5.40940.29621450.224613191464100
5.4094-6.81130.24281510.24971347149899
6.8113-44.32210.19421440.18291348149299

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