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- PDB-8re2: Crystal Structure determination of Dye-decolorizing Peroxidase (D... -

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Basic information

Entry
Database: PDB / ID: 8re2
TitleCrystal Structure determination of Dye-decolorizing Peroxidase (DyP) from Deinoccoccus radiodurans
ComponentsPeroxidase, putative
KeywordsSTRUCTURAL PROTEIN / Heme protein / peroxidase / ferredoxin like fold / Hydrogen Peroxide
Function / homologyDyP dimeric alpha+beta barrel domain / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel / peroxidase activity / heme binding / cytosol / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase, putative
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSalgueiro, B.A. / Frade, K. / Frazao, C. / Moe, E.
Funding support Portugal, 6items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)PTDC/BBBEBB/0122/2014 Portugal
Foundation for Science and Technology (FCT)SFRH/BPD/97493/2013 Portugal
Foundation for Science and Technology (FCT)COVID/BD/152598/2022 Portugal
Foundation for Science and Technology (FCT)UIDB/04612/2020 Portugal
Foundation for Science and Technology (FCT)UIDP/04612/2020 Portugal
Foundation for Science and Technology (FCT)LA/P/0087/2020 Portugal
CitationJournal: Molecules / Year: 2024
Title: Biochemical, Biophysical, and Structural Analysis of an Unusual DyP from the Extremophile Deinococcus radiodurans.
Authors: Frade, K. / Silveira, C.M. / Salgueiro, B.A. / Mendes, S. / Martins, L.O. / Frazao, C. / Todorovic, S. / Moe, E.
History
DepositionDec 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3757
Polymers49,5021
Non-polymers8746
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.130, 64.130, 111.322
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Peroxidase, putative /


Mass: 49501.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_A0145 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): * / References: UniProt: Q9RZ08
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8.5 / Details: 18% PEG 8000, 0.1 M CHES pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→55.54 Å / Num. obs: 25843 / % possible obs: 99.5 % / Redundancy: 4.02 % / Biso Wilson estimate: 62.2 Å2 / Rpim(I) all: 0.0352 / Rsym value: 0.066 / Net I/σ(I): 10.96
Reflection shellResolution: 2.2→2.33 Å / Num. unique obs: 4160 / Rpim(I) all: 0.347 / Rsym value: 1.08

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
XDSdata reduction
XDSdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.31 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 32.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2374 1996 7.73 %
Rwork0.1832 --
obs0.1875 25834 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 58 49 3599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083640
X-RAY DIFFRACTIONf_angle_d0.9634941
X-RAY DIFFRACTIONf_dihedral_angle_d9.939492
X-RAY DIFFRACTIONf_chiral_restr0.055509
X-RAY DIFFRACTIONf_plane_restr0.01648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.39821350.36021675X-RAY DIFFRACTION98
2.26-2.320.35841480.3221698X-RAY DIFFRACTION100
2.32-2.380.35361480.27571728X-RAY DIFFRACTION100
2.38-2.460.32961460.26831715X-RAY DIFFRACTION100
2.46-2.550.32671360.25151684X-RAY DIFFRACTION100
2.55-2.650.30311460.22841730X-RAY DIFFRACTION100
2.65-2.770.25661450.21271706X-RAY DIFFRACTION100
2.77-2.920.33361460.25061726X-RAY DIFFRACTION100
2.92-3.10.28371330.22741687X-RAY DIFFRACTION100
3.1-3.340.26951440.20881719X-RAY DIFFRACTION100
3.34-3.680.24731400.19691702X-RAY DIFFRACTION99
3.68-4.210.22941460.16011686X-RAY DIFFRACTION99
4.21-5.30.18731380.13831695X-RAY DIFFRACTION99
5.3-39.310.17311450.13341687X-RAY DIFFRACTION99

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