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- PDB-6y1t: The crystal structure of engineered cytochrome c peroxidase from ... -

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Basic information

Entry
Database: PDB / ID: 6y1t
TitleThe crystal structure of engineered cytochrome c peroxidase from Saccharomyces cerevisiae with a Trp51 to S-Trp51 modification
ComponentsCytochrome c peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE / Peroxidase / heme / engineered / non-canonical amino acid
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 S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsOrtmayer, M. / Levy, C. / Green, A.P.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
European Research Council (ERC) United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: Jacs Au / Year: 2021
Title: A Noncanonical Tryptophan Analogue Reveals an Active Site Hydrogen Bond Controlling Ferryl Reactivity in a Heme Peroxidase.
Authors: Ortmayer, M. / Hardy, F.J. / Quesne, M.G. / Fisher, K. / Levy, C. / Heyes, D.J. / Catlow, C.R.A. / de Visser, S.P. / Rigby, S.E.J. / Hay, S. / Green, A.P.
History
DepositionFeb 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Advisory / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / diffrn_source / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)37,6794
Polymers36,7621
Non-polymers9173
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-22 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.848, 75.191, 106.981
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: 36761.730 Da / Num. of mol.: 1 / Mutation: Trp51S-Trp
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: CCP1, CCP, CPO, YKR066C / Production host: Escherichia coli (E. coli) / 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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 60 mM magnesium chloride hexahydrate, 60 mM calcuim chloride dihydrate, 0.1 M imidazole, 0.1 M MES pH 6.5, 20% v/v ethylene glycol and 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→39.19 Å / Num. obs: 65800 / % possible obs: 99 % / Redundancy: 5.5 % / Biso Wilson estimate: 16.17 Å2 / Rrim(I) all: 0.09279 / Net I/σ(I): 9.07
Reflection shellResolution: 1.5→1.52 Å / Rmerge(I) obs: 0.5268 / Num. unique obs: 2251

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CYP

2cyp


Resolution: 1.5→35.47 Å / SU ML: 0.1612 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7866
RfactorNum. reflection% reflection
Rfree0.1766 3277 4.97 %
Rwork0.1467 --
obs0.1489 65800 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.41 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 72 411 2827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762556
X-RAY DIFFRACTIONf_angle_d1.01733477
X-RAY DIFFRACTIONf_chiral_restr0.0733337
X-RAY DIFFRACTIONf_plane_restr0.0062457
X-RAY DIFFRACTIONf_dihedral_angle_d19.5948348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.28081060.26562251X-RAY DIFFRACTION82.73
1.52-1.540.28791340.23982561X-RAY DIFFRACTION93.77
1.54-1.570.28671190.21922650X-RAY DIFFRACTION97.43
1.57-1.60.23831530.20272723X-RAY DIFFRACTION99.28
1.6-1.630.22641320.18542687X-RAY DIFFRACTION99.86
1.63-1.660.22621450.17662714X-RAY DIFFRACTION99.97
1.66-1.690.24691500.17352748X-RAY DIFFRACTION99.97
1.69-1.730.20591570.15232690X-RAY DIFFRACTION100
1.73-1.770.18651420.15412713X-RAY DIFFRACTION99.96
1.77-1.810.21041490.14822731X-RAY DIFFRACTION99.97
1.81-1.860.19781520.14532721X-RAY DIFFRACTION99.97
1.86-1.920.19311570.14222733X-RAY DIFFRACTION100
1.92-1.980.17561310.13722763X-RAY DIFFRACTION100
1.98-2.050.17831350.13932739X-RAY DIFFRACTION100
2.05-2.130.14561330.1252744X-RAY DIFFRACTION100
2.13-2.230.14721470.11962769X-RAY DIFFRACTION100
2.23-2.340.16151330.11882758X-RAY DIFFRACTION99.97
2.34-2.490.14071520.12452741X-RAY DIFFRACTION100
2.49-2.680.15271520.1292797X-RAY DIFFRACTION100
2.68-2.950.16221370.14112784X-RAY DIFFRACTION100
2.95-3.380.18981480.14992803X-RAY DIFFRACTION100
3.38-4.260.15181440.14242844X-RAY DIFFRACTION100
4.26-35.470.17591690.16322949X-RAY DIFFRACTION99.9

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