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- PDB-5ejx: X-ray Free Electron Laser Structure of Cytochrome C Peroxidase -

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Basic information

Entry
Database: PDB / ID: 5ejx
TitleX-ray Free Electron Laser Structure of Cytochrome C Peroxidase
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.4Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.470, 74.990, 51.250
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: N184R
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.: 293 / 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: 60.3 %
Description: Multiple rectangular crystals used, approximately 200 x 200 x 400 micron
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: 4C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.306, 1.313
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: Dec 7, 2013
Details: Data collected over two experiments, in Dec 2013 and June 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.3061
21.3131
ReflectionResolution: 1.5→19.7 Å / Num. all: 65592 / Num. obs: 65592 / % possible obs: 97.8 % / Redundancy: 9.2 % / Net I/σ(I): 3.33
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSnXDSdata reduction
XSCALE2015-06-17data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M23

3m23


Resolution: 1.5→19.69 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.852 / SU B: 1.758 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26055 3280 5 %RANDOM
Rwork0.23384 ---
obs0.23518 62310 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.141 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.5→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 48 293 2693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192547
X-RAY DIFFRACTIONr_bond_other_d0.0020.022306
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.9683461
X-RAY DIFFRACTIONr_angle_other_deg1.1435331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1855306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4324.733131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6915423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3411512
X-RAY DIFFRACTIONr_chiral_restr0.1310.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212981
X-RAY DIFFRACTIONr_gen_planes_other0.010.02627
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5660.4051203
X-RAY DIFFRACTIONr_mcbond_other0.5650.4041202
X-RAY DIFFRACTIONr_mcangle_it0.9330.6051516
X-RAY DIFFRACTIONr_mcangle_other0.9330.6051517
X-RAY DIFFRACTIONr_scbond_it1.160.4911344
X-RAY DIFFRACTIONr_scbond_other1.1580.4851338
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.740.6921939
X-RAY DIFFRACTIONr_long_range_B_refined3.8953.9793359
X-RAY DIFFRACTIONr_long_range_B_other3.2763.5453205
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 222 -
Rwork0.288 4207 -
obs--90.91 %

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