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- PDB-5ejt: Thermally annealed ferryl Cytochrome C Peroxidase crystal structure -

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Basic information

Entry
Database: PDB / ID: 5ejt
TitleThermally annealed ferryl Cytochrome C Peroxidase crystal structure
ComponentsCytochrome c peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE
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 / 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. ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsDoukov, T. / Soltis, S.M. / Baxter, E.L. / Cohen, A. / Song, J. / McPhillips, S. / Poulos, T.L. / Meharenna, Y.T. / Chreifi, G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM57353 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Crystal structure of the pristine peroxidase ferryl center and its relevance to proton-coupled electron transfer.
Authors: Chreifi, G. / Baxter, E.L. / Doukov, T. / Cohen, A.E. / McPhillips, S.E. / Song, J. / Meharenna, Y.T. / Soltis, S.M. / Poulos, T.L.
History
DepositionNov 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 17, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,3263
Polymers33,6141
Non-polymers7112
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.330, 75.190, 51.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33614.332 Da / Num. of mol.: 1 / Mutation: R184N
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 / Organ: mitochondrialMitochondrion / Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 60.31 %
Description: rectangular shape with 200 by 200 by 150 microns distances
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10UL (350-400UM PROTEIN), 22% MPD, 50MM TRIS PHOSHATE BUFFER PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.2K
PH range: 6 / Temp details: 4 C

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: Collected perviously to 8.6 MGy absorbed dose, thermally anneled and collected 360 degrees dataset to final absorbed dose 11.5 MGy
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.55→39.35 Å / Num. all: 60803 / Num. obs: 60803 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 19.87 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.124 / Net I/σ(I): 14.5
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 9 % / Rmerge(I) obs: 2.493 / Mean I/σ(I) obs: 0.8 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSMarch 1, 2015data reduction
Aimless0.5.8data scaling
PHASER2.5.6phasing
RefinementResolution: 1.55→39.35 Å / Cor.coef. Fo:Fc: 0.9634 / Cor.coef. Fo:Fc free: 0.9562 / SU R Cruickshank DPI: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.065 / SU Rfree Cruickshank DPI: 0.061
RfactorNum. reflection% reflectionSelection details
Rfree0.1766 3079 5.08 %RANDOM
Rwork0.153 ---
obs0.1541 60637 99.68 %-
Displacement parametersBiso mean: 24.47 Å2
Baniso -1Baniso -2Baniso -3
1-4.2033 Å20 Å20 Å2
2---4.2502 Å20 Å2
3---0.0469 Å2
Refine analyzeLuzzati coordinate error obs: 0.165 Å
Refinement stepCycle: 1 / Resolution: 1.55→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 48 537 3019
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012560HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.893486HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1165SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes365HARMONIC5
X-RAY DIFFRACTIONt_it2560HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.89
X-RAY DIFFRACTIONt_other_torsion2.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion293SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3497SEMIHARMONIC4
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2682 215 5.06 %
Rwork0.2594 4030 -
all0.2598 4245 -
obs--99.68 %
Refinement TLS params.Method: refined / Origin x: 21.6896 Å / Origin y: 88.6339 Å / Origin z: 52.6397 Å
111213212223313233
T-0.0329 Å20.0094 Å2-0.0008 Å2--0.0382 Å20.0129 Å2---0.0407 Å2
L1.2156 °2-0.0399 °20.1023 °2-0.4615 °20.0032 °2--0.4555 °2
S-0.0423 Å °0.0306 Å °0.118 Å °0.0209 Å °0.0347 Å °0.0123 Å °-0.0638 Å °-0.0015 Å °0.0076 Å °
Refinement TLS groupSelection details: { A|* }

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