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- PDB-9c8m: High-resolution structure of cytochrome c peroxidase from yeast u... -

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Basic information

Entry
Database: PDB / ID: 9c8m
TitleHigh-resolution structure of cytochrome c peroxidase from yeast under cryogenic conditions and ambient pressure
ComponentsCytochrome c peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE / Electron transfer / hydrogen peroxide / high-pressure / diamond anvil cell / peroxidase / cytochrome
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: 1.78 Å
AuthorsZawistowski, R.K. / Crane, B.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)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
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.605, 72.888, 100.378
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.: 319 / 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: 2.42 Å3/Da / Density % sol: 49.09 % / 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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.78→41.34 Å / Num. obs: 31873 / % possible obs: 99.52 % / Redundancy: 26.4 % / Biso Wilson estimate: 24.65 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.022 / Rrim(I) all: 0.109 / Χ2: 1.546 / Net I/σ(I): 58.18
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.909 / Mean I/σ(I) obs: 3.65 / Num. unique obs: 1516 / CC1/2: 0.91 / CC star: 0.976 / Rpim(I) all: 0.218 / Rrim(I) all: 0.936 / Χ2: 0.719 / % possible all: 97.74

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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: 1.78→41.34 Å / SU ML: 0.2132 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.8477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2131 2000 6.27 %
Rwork0.1726 29873 -
obs0.1751 31873 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.87 Å2
Refinement stepCycle: LAST / Resolution: 1.78→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 43 319 2736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622506
X-RAY DIFFRACTIONf_angle_d0.86223414
X-RAY DIFFRACTIONf_chiral_restr0.0487337
X-RAY DIFFRACTIONf_plane_restr0.0064448
X-RAY DIFFRACTIONf_dihedral_angle_d16.222906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.830.31611380.27012060X-RAY DIFFRACTION98.34
1.83-1.880.31171400.23432093X-RAY DIFFRACTION99.69
1.88-1.930.26571420.20652121X-RAY DIFFRACTION99.78
1.93-1.990.21771400.18692096X-RAY DIFFRACTION99.87
1.99-2.060.2341420.18762111X-RAY DIFFRACTION99.91
2.06-2.150.21951430.19092130X-RAY DIFFRACTION99.96
2.15-2.240.23331410.19632118X-RAY DIFFRACTION99.91
2.24-2.360.25191420.18852120X-RAY DIFFRACTION99.74
2.36-2.510.23731430.17992137X-RAY DIFFRACTION99.82
2.51-2.710.17841430.17472132X-RAY DIFFRACTION99.91
2.71-2.980.2331440.18012152X-RAY DIFFRACTION99.52
2.98-3.410.24141440.17632155X-RAY DIFFRACTION99.48
3.41-4.290.18291440.14492157X-RAY DIFFRACTION98.29
4.29-41.340.16561540.1462291X-RAY DIFFRACTION99.23

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