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- PDB-7biu: XFEL crystal structure of cytochrome c peroxidase compound II -

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Basic information

Entry
Database: PDB / ID: 7biu
TitleXFEL crystal structure of cytochrome c peroxidase compound II
ComponentsCytochrome c peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE / Intermediates / Heme protein
Function / homology
Function and homology information


Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / response to oxidative stress / membrane => GO:0016020 / heme binding / metal ion binding
Similarity search - Function
Class I peroxidase / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsKwon, H. / Tosha, T. / Sugimoto, H. / Raven, E.L. / Moody, P.C.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N015940/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: XFEL Crystal Structures of Peroxidase Compound II.
Authors: Kwon, H. / Basran, J. / Pathak, C. / Hussain, M. / Freeman, S.L. / Fielding, A.J. / Bailey, A.J. / Stefanou, N. / Sparkes, H.A. / Tosha, T. / Yamashita, K. / Hirata, K. / Murakami, H. / ...Authors: Kwon, H. / Basran, J. / Pathak, C. / Hussain, M. / Freeman, S.L. / Fielding, A.J. / Bailey, A.J. / Stefanou, N. / Sparkes, H.A. / Tosha, T. / Yamashita, K. / Hirata, K. / Murakami, H. / Ueno, G. / Ago, H. / Tono, K. / Yamamoto, M. / Sawai, H. / Shiro, Y. / Sugimoto, H. / Raven, E.L. / Moody, P.C.E.
History
DepositionJan 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 31, 2024Group: 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)34,2482
Polymers33,6291
Non-polymers6191
Water9,998555
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-21 kcal/mol
Surface area12340 Å2
Unit cell
Length a, b, c (Å)50.810, 75.540, 106.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome c peroxidase, mitochondrial /


Mass: 33629.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCNYR20_0010026000, SCP684_0010026400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6V8S829
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 277 K / Method: microdialysis / Details: 30 % MPD, 50 mM K phosphate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 0.82 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82 Å / Relative weight: 1
ReflectionResolution: 1.06→13 Å / Num. obs: 185757 / % possible obs: 100 % / Redundancy: 377 % / CC1/2: 0.97 / Net I/σ(I): 6.34
Reflection shellResolution: 1.06→1.07 Å / Num. unique obs: 10303 / CC1/2: 0.25

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Processing

Software
NameVersionClassification
SHELXrefinement
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CVJ

4cvj


Resolution: 1.06→13 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rwork0.14 --
obs-41508 100 %
Displacement parametersBiso max: 167.91 Å2 / Biso mean: 20.5726 Å2 / Biso min: 5.99 Å2
Refinement stepCycle: LAST / Resolution: 1.06→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 43 555 2951

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