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- PDB-9c8p: High-resolution structure of cytochrome c peroxidase from yeast a... -

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Basic information

Entry
Database: PDB / ID: 9c8p
TitleHigh-resolution structure of cytochrome c peroxidase from yeast at ambient temperature and 3.0 kbar
ComponentsCytochrome c peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE / Electron transfer / hydrogen peroxide / high-pressure / diamond anvil cell / peroxidase / cytochrome / heme
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / 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
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsZawistowski, R.K. / Crane, B.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF MCB 2129729 to BRC United States
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Differential Responses in the Core, Active Site and Peripheral Regions of Cytochrome c Peroxidase to Extreme Pressure and Temperature.
Authors: Zawistowski, R.K. / Crane, B.R.
History
DepositionJun 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3862
Polymers33,7701
Non-polymers6161
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.711, 74.253, 101.312
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cytochrome c peroxidase, mitochondrial / CCP


Mass: 33769.605 Da / Num. of mol.: 1
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.49 Å3/Da / Density % sol: 50.6 % / Description: red, long and rod-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10-25 % polyethylene glycol 550 (MME) and 100 mM 2-(N-morpholino)ethanesulfonic acid (pH 6.1-7.1)
PH range: 6.1-7.1

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.7847 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7847 Å / Relative weight: 1
ReflectionResolution: 2.31→27.49 Å / Num. obs: 14623 / % possible obs: 95.03 % / Redundancy: 5.5 % / Biso Wilson estimate: 26.2 Å2 / CC1/2: 0.973 / CC star: 0.993 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.082 / Rrim(I) all: 0.2 / Net I/σ(I): 7.2
Reflection shellResolution: 2.31→2.37 Å / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2 / Num. unique obs: 1096 / CC1/2: 0.651 / CC star: 0.888 / Rpim(I) all: 0.298 / Rrim(I) all: 0.725 / % possible all: 93.36

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Coot0.9.8.92model building
HKL-2000v722data scaling
PHENIX1.21_5207phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→27.49 Å / SU ML: 0.3085 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.7464
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2731 1461 9.99 %
Rwork0.217 13162 -
obs0.2226 14623 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.5 Å2
Refinement stepCycle: LAST / Resolution: 2.31→27.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 43 221 2597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222465
X-RAY DIFFRACTIONf_angle_d0.52653369
X-RAY DIFFRACTIONf_chiral_restr0.038336
X-RAY DIFFRACTIONf_plane_restr0.0035445
X-RAY DIFFRACTIONf_dihedral_angle_d15.9914869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.390.33821400.27481262X-RAY DIFFRACTION93.16
2.39-2.490.35481430.28641285X-RAY DIFFRACTION94.26
2.49-2.60.36941420.28181281X-RAY DIFFRACTION94.8
2.6-2.740.31721460.26451302X-RAY DIFFRACTION95.7
2.74-2.910.29951450.26951319X-RAY DIFFRACTION95.87
2.91-3.130.30071470.24941316X-RAY DIFFRACTION96.31
3.13-3.450.29281480.23481328X-RAY DIFFRACTION95.91
3.45-3.950.24291470.18571318X-RAY DIFFRACTION94.52
3.95-4.970.23261480.16981348X-RAY DIFFRACTION95.41
4.97-27.490.19981550.15841403X-RAY DIFFRACTION94.37

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