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- PDB-7zcl: Unspecific peroxygenase from Collariella virescens -

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Basic information

Entry
Database: PDB / ID: 7zcl
TitleUnspecific peroxygenase from Collariella virescens
Components(Collariella virescens UPO) x 2
KeywordsOXIDOREDUCTASE / Unspecific peroxygenases (UPO) / Collariella virescens / Short UPO family / Molecular structure / Fatty acid epoxidation
Function / homologyHEME C
Function and homology information
Biological speciesCollariella virescens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSantillana, E. / Romero, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish National Research CouncilPIE-202020E224 Spain
CitationJournal: Antioxidants / Year: 2022
Title: Structural Characterization of Two Short Unspecific Peroxygenases: Two Different Dimeric Arrangements.
Authors: Linde, D. / Santillana, E. / Fernandez-Fueyo, E. / Gonzalez-Benjumea, A. / Carro, J. / Gutierrez, A. / Martinez, A.T. / Romero, A.
History
DepositionMar 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collariella virescens UPO
B: Collariella virescens UPO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2046
Polymers51,9182
Non-polymers1,2864
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-94 kcal/mol
Surface area19100 Å2
Unit cell
Length a, b, c (Å)78.476, 140.131, 42.227
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Collariella virescens UPO


Mass: 25923.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Collariella virescens (fungus) / Production host: Escherichia coli (E. coli) / References: unspecific peroxygenase
#2: Protein Collariella virescens UPO


Mass: 25994.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Collariella virescens (fungus) / Production host: Escherichia coli (E. coli) / References: unspecific peroxygenase
#3: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 400, 0.1 M Tris, pH 8.5, 0.2 M sodium citrate

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.95→70.1 Å / Num. obs: 35859 / % possible obs: 100 % / Redundancy: 8.7 % / Biso Wilson estimate: 22.28 Å2 / Rpim(I) all: 0.057 / Rrim(I) all: 0.191 / Net I/σ(I): 10.1
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5682 / Rpim(I) all: 0.4 / Rrim(I) all: 0.99 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YOR

2yor


Resolution: 1.95→68.47 Å / SU ML: 0.2163 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.3086
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 1754 5 %RANDOM
Rwork0.1877 33333 --
obs0.1903 35087 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.54 Å2
Refinement stepCycle: LAST / Resolution: 1.95→68.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3657 0 88 268 4013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813857
X-RAY DIFFRACTIONf_angle_d1.03245256
X-RAY DIFFRACTIONf_chiral_restr0.0599549
X-RAY DIFFRACTIONf_plane_restr0.0094670
X-RAY DIFFRACTIONf_dihedral_angle_d9.9068509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.36251130.31382545X-RAY DIFFRACTION99.77
2-2.060.31751540.25422485X-RAY DIFFRACTION100
2.06-2.120.28521380.21572552X-RAY DIFFRACTION99.96
2.12-2.20.26981400.19082486X-RAY DIFFRACTION100
2.2-2.290.23971350.18272531X-RAY DIFFRACTION99.96
2.29-2.390.22521040.17812566X-RAY DIFFRACTION99.93
2.39-2.520.26231310.17612552X-RAY DIFFRACTION99.96
2.52-2.670.25551300.18112541X-RAY DIFFRACTION100
2.67-2.880.25591470.18762560X-RAY DIFFRACTION100
2.88-3.170.25691190.19312566X-RAY DIFFRACTION100
3.17-3.630.22821270.1822603X-RAY DIFFRACTION99.96
3.63-4.570.19811540.16042611X-RAY DIFFRACTION99.96
4.57-68.470.21851620.1792735X-RAY DIFFRACTION99.79

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