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- PDB-7zbp: Unspecific peroxygenase from Marasmius rotula -

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Basic information

Entry
Database: PDB / ID: 7zbp
TitleUnspecific peroxygenase from Marasmius rotula
ComponentsMarasmius rotula UPO
KeywordsOXIDOREDUCTASE / Unspecific peroxygenases (UPO) / Marasmius rotula / Short UPO family / Molecular structure / Fatty acid epoxidation
Function / homologyACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMarasmius rotula (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 24, 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

Downloads & links

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Assembly

Deposited unit
A: Marasmius rotula UPO
B: Marasmius rotula UPO
C: Marasmius rotula UPO
D: Marasmius rotula UPO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,82419
Polymers103,7214
Non-polymers3,10415
Water19,0601058
1
A: Marasmius rotula UPO
B: Marasmius rotula UPO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,56411
Polymers51,8602
Non-polymers1,7049
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-85 kcal/mol
Surface area19450 Å2
MethodPISA
2
C: Marasmius rotula UPO
D: Marasmius rotula UPO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2608
Polymers51,8602
Non-polymers1,4006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-91 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.349, 107.440, 186.231
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-667-

HOH

21B-696-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Marasmius rotula UPO


Mass: 25930.170 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marasmius rotula (fungus) / Production host: Escherichia coli (E. coli) / References: unspecific peroxygenase

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Non-polymers , 6 types, 1073 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1058 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 20% PEG 3000, 0.1 M sodium acetate, pH 4.5

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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: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.45→73.44 Å / Num. obs: 175829 / % possible obs: 99.4 % / Redundancy: 6.1 % / Rpim(I) all: 0.037 / Rrim(I) all: 0.094 / Net I/σ(I): 12
Reflection shellResolution: 1.45→1.55 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 25506 / Rpim(I) all: 0.33 / Rrim(I) all: 0.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YOR

2yor


Resolution: 1.45→73.44 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.252 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 8668 4.9 %RANDOM
Rwork0.1579 ---
obs0.1592 167101 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.42 Å2 / Biso mean: 16.605 Å2 / Biso min: 5.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å2-0 Å20 Å2
2--0.05 Å20 Å2
3----0.98 Å2
Refinement stepCycle: final / Resolution: 1.45→73.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7274 0 211 1058 8543
Biso mean--14.4 28.47 -
Num. residues----953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0137664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177008
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.68510477
X-RAY DIFFRACTIONr_angle_other_deg1.561.59416267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5725949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.35622.296379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57151199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.691552
X-RAY DIFFRACTIONr_chiral_restr0.0980.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.028667
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021573
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 667 -
Rwork0.27 12200 -
all-12867 -
obs--99.31 %

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