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- PDB-4w7k: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICUL... -

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Basic information

Entry
Database: PDB / ID: 4w7k
TitleCRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S MUTANT
ComponentsDye-decolorizing peroxidase
KeywordsOXIDOREDUCTASE / DECOLORIZING PEROXIDASE (DYP) / HEME
Function / homology
Function and homology information


dye decolorizing peroxidase / peroxidase / lactoperoxidase activity / peroxidase activity / heme binding / extracellular region / metal ion binding / cytosol
Similarity search - Function
: / DyP dimeric alpha+beta barrel domain / : / 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 / Dye-decolorizing peroxidase AauDyP1
Similarity search - Component
Biological speciesAuricularia auricula-judae (jelly ear fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsMedrano, F.J. / Romero, A.
CitationJournal: Biochem.J. / Year: 2015
Title: Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study.
Authors: Linde, D. / Pogni, R. / Canellas, M. / Lucas, F. / Guallar, V. / Baratto, M.C. / Sinicropi, A. / Saez-Jimenez, V. / Coscolin, C. / Romero, A. / Medrano, F.J. / Ruiz-Duenas, F.J. / Martinez, A.T.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dye-decolorizing peroxidase
B: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2954
Polymers94,0622
Non-polymers1,2332
Water26,6081477
1
A: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6482
Polymers47,0311
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6482
Polymers47,0311
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.950, 55.870, 104.000
Angle α, β, γ (deg.)90.00, 118.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

21B-684-

HOH

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Components

#1: Protein Dye-decolorizing peroxidase


Mass: 47031.207 Da / Num. of mol.: 2 / Fragment: UNP residues 62-509 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Auricularia auricula-judae (jelly ear fungus)
Gene: dyp1 / Production host: Escherichia coli (E. coli) / References: UniProt: I2DBY1, dye decolorizing peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1477 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 35% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.00791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00791 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 364516 / % possible obs: 82.6 % / Redundancy: 6 % / Net I/σ(I): 12.3
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 1 / % possible all: 29.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AFV

4afv


Resolution: 1.05→33.627 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1568 18260 5.02 %
Rwork0.1354 --
obs0.1364 364071 82.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→33.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6596 0 86 1477 8159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096975
X-RAY DIFFRACTIONf_angle_d1.419545
X-RAY DIFFRACTIONf_dihedral_angle_d14.5152473
X-RAY DIFFRACTIONf_chiral_restr0.0811054
X-RAY DIFFRACTIONf_plane_restr0.0091274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0437-1.05550.3321710.38771273X-RAY DIFFRACTION9
1.0555-1.06790.31221840.30443387X-RAY DIFFRACTION25
1.0679-1.0810.31972330.27854509X-RAY DIFFRACTION32
1.081-1.09460.30173180.25735537X-RAY DIFFRACTION40
1.0946-1.1090.25523500.24286631X-RAY DIFFRACTION48
1.109-1.12420.26344360.23057802X-RAY DIFFRACTION56
1.1242-1.14030.23374870.21088798X-RAY DIFFRACTION63
1.1403-1.15730.22895150.19179888X-RAY DIFFRACTION72
1.1573-1.17540.20625880.184511172X-RAY DIFFRACTION81
1.1754-1.19470.20386650.174612696X-RAY DIFFRACTION91
1.1947-1.21530.2027120.167313356X-RAY DIFFRACTION96
1.2153-1.23740.18526950.155213350X-RAY DIFFRACTION96
1.2374-1.26120.1697000.14813439X-RAY DIFFRACTION97
1.2612-1.28690.18287110.149913443X-RAY DIFFRACTION97
1.2869-1.31490.17587130.140913523X-RAY DIFFRACTION97
1.3149-1.34550.17057080.138913480X-RAY DIFFRACTION97
1.3455-1.37910.1597100.131313564X-RAY DIFFRACTION98
1.3791-1.41640.15117150.121713613X-RAY DIFFRACTION98
1.4164-1.45810.14357160.117913676X-RAY DIFFRACTION98
1.4581-1.50520.13877170.115613618X-RAY DIFFRACTION98
1.5052-1.5590.14377220.110213674X-RAY DIFFRACTION98
1.559-1.62140.14657220.108913734X-RAY DIFFRACTION99
1.6214-1.69520.13447220.11313804X-RAY DIFFRACTION99
1.6952-1.78460.1387280.117713811X-RAY DIFFRACTION99
1.7846-1.89640.15417310.125313869X-RAY DIFFRACTION99
1.8964-2.04280.14247330.124713925X-RAY DIFFRACTION100
2.0428-2.24830.13727340.120413977X-RAY DIFFRACTION100
2.2483-2.57350.13927380.12713990X-RAY DIFFRACTION100
2.5735-3.24190.16097400.142814047X-RAY DIFFRACTION100
3.2419-33.64470.157460.136614225X-RAY DIFFRACTION99

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