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- PDB-4w7j: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICUL... -

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Basic information

Entry
Database: PDB / ID: 4w7j
TitleCRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE
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: 1.79 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 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
C: Dye-decolorizing peroxidase
D: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,8958
Polymers188,4294
Non-polymers2,4664
Water22,1761231
1
A: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7242
Polymers47,1071
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7242
Polymers47,1071
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7242
Polymers47,1071
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7242
Polymers47,1071
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.220, 100.500, 128.630
Angle α, β, γ (deg.)90.00, 123.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-640-

HOH

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Components

#1: Protein
Dye-decolorizing peroxidase


Mass: 47107.305 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1231 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 32.5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 150630 / % possible obs: 97.1 % / Redundancy: 4.1 % / Net I/σ(I): 6.59
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.995 / Mean I/σ(I) obs: 1.03 / % possible all: 90.3

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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: 1.79→39.356 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 7496 4.99 %
Rwork0.1935 --
obs0.1959 150153 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→39.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13211 0 172 1231 14614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713723
X-RAY DIFFRACTIONf_angle_d1.07618786
X-RAY DIFFRACTIONf_dihedral_angle_d13.914798
X-RAY DIFFRACTIONf_chiral_restr0.0422084
X-RAY DIFFRACTIONf_plane_restr0.0062503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.80550.48851530.43722971X-RAY DIFFRACTION60
1.8055-1.82670.38232500.33114759X-RAY DIFFRACTION98
1.8267-1.8490.35052450.30634816X-RAY DIFFRACTION98
1.849-1.87240.34142510.29214714X-RAY DIFFRACTION98
1.8724-1.89710.35912500.28034838X-RAY DIFFRACTION98
1.8971-1.9230.33322410.26284758X-RAY DIFFRACTION98
1.923-1.95050.30942510.23944777X-RAY DIFFRACTION98
1.9505-1.97960.2682720.23344748X-RAY DIFFRACTION98
1.9796-2.01060.30282500.23164842X-RAY DIFFRACTION98
2.0106-2.04350.26912540.22434795X-RAY DIFFRACTION98
2.0435-2.07880.27712410.21484800X-RAY DIFFRACTION98
2.0788-2.11660.26472660.20014778X-RAY DIFFRACTION98
2.1166-2.15730.25652580.19114789X-RAY DIFFRACTION98
2.1573-2.20130.24142490.19144822X-RAY DIFFRACTION98
2.2013-2.24910.25622560.19534811X-RAY DIFFRACTION98
2.2491-2.30150.26382500.19774834X-RAY DIFFRACTION98
2.3015-2.3590.28962400.19464824X-RAY DIFFRACTION99
2.359-2.42280.24312590.18194823X-RAY DIFFRACTION99
2.4228-2.49410.25462570.18264824X-RAY DIFFRACTION98
2.4941-2.57460.24952560.1874812X-RAY DIFFRACTION98
2.5746-2.66650.23732610.19694810X-RAY DIFFRACTION99
2.6665-2.77330.25482450.19224871X-RAY DIFFRACTION99
2.7733-2.89950.2572500.19774826X-RAY DIFFRACTION99
2.8995-3.05230.2382570.19454860X-RAY DIFFRACTION99
3.0523-3.24340.23762540.1964862X-RAY DIFFRACTION99
3.2434-3.49370.22892590.18064844X-RAY DIFFRACTION99
3.4937-3.8450.19082580.16534873X-RAY DIFFRACTION99
3.845-4.40080.17342550.14844845X-RAY DIFFRACTION98
4.4008-5.54210.18412500.15314843X-RAY DIFFRACTION98
5.5421-39.36550.20792580.17224888X-RAY DIFFRACTION97

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