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- PDB-8ohy: Native Structure of Dictyostelium discoideum dye-decolorizing per... -

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Basic information

Entry
Database: PDB / ID: 8ohy
TitleNative Structure of Dictyostelium discoideum dye-decolorizing peroxidase
ComponentsPeroxidase
KeywordsHYDROLASE / Dye-decolorizing peroxidase / H2O2-dependent oxidation / lignin degradation / hydrolysis / heme peroxidase
Function / homology
Function and homology information


peroxidase activity / protein dimerization activity / heme binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Dyp-type peroxidase family protein
Similarity search - Component
Biological speciesDictyostelium discoideum AX4 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKoua, F.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Chem / Year: 2023
Title: Heterologous expression, purification and structural features of native Dictyostelium discoideum dye-decolorizing peroxidase bound to a natively incorporated heme.
Authors: Kalkan, O. / Kantamneni, S. / Brings, L. / Han, H. / Bean, R. / Mancuso, A.P. / Koua, F.H.M.
History
DepositionMar 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6973
Polymers35,0151
Non-polymers6822
Water2,864159
1
A: Peroxidase
hetero molecules

A: Peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3946
Polymers70,0302
Non-polymers1,3644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area5330 Å2
ΔGint-108 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.880, 99.880, 73.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Peroxidase


Mass: 35014.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum AX4 (eukaryote)
Gene: DDB0168077, DDB0217308 / Production host: Escherichia coli (E. coli) / References: UniProt: Q556V8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: HEPES-NaOH, PEG 6000, ZnCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.95→44.67 Å / Num. obs: 27351 / % possible obs: 98.54 % / Redundancy: 26.7 % / Biso Wilson estimate: 36.83 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.2715 / Net I/σ(I): 12.02
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 26 % / Rmerge(I) obs: 4.643 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2472 / CC1/2: 0.411 / CC star: 0.764 / % possible all: 91.55

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Processing

Software
NameVersionClassification
PHENIX(1.20-4459_9999: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→44.67 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 1114 4.11 %
Rwork0.2044 --
obs0.2062 27129 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 44 159 2662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032556
X-RAY DIFFRACTIONf_angle_d0.6583456
X-RAY DIFFRACTIONf_dihedral_angle_d13.47975
X-RAY DIFFRACTIONf_chiral_restr0.042370
X-RAY DIFFRACTIONf_plane_restr0.006443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.040.41941300.38363018X-RAY DIFFRACTION93
2.04-2.150.35371350.30653161X-RAY DIFFRACTION98
2.15-2.280.30021390.24063247X-RAY DIFFRACTION100
2.28-2.460.25561380.21223230X-RAY DIFFRACTION100
2.46-2.70.25581410.18993283X-RAY DIFFRACTION100
2.7-3.10.22221400.19313290X-RAY DIFFRACTION100
3.1-3.90.23591420.18323318X-RAY DIFFRACTION100
3.9-44.670.22941490.18863468X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 2.0963 Å / Origin y: 23.1975 Å / Origin z: -17.3159 Å
111213212223313233
T0.2031 Å2-0.008 Å20.012 Å2-0.1879 Å2-0.0248 Å2--0.3736 Å2
L1.212 °20.3074 °2-0.1627 °2-0.9898 °20.1014 °2--1.6396 °2
S0.0879 Å °-0.1692 Å °0.1808 Å °0.0484 Å °-0.023 Å °-0.0124 Å °-0.1478 Å °0.0629 Å °-0.0598 Å °
Refinement TLS groupSelection details: all

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