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- PDB-4w7n: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICUL... -

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Basic information

Entry
Database: PDB / ID: 4w7n
TitleCRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S AND W377S DOUBLE MUTANT
ComponentsDye-decolorizing peroxidase
KeywordsOXIDOREDUCTASE / HEME / GLYCOPROTEIN
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: 1.401 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,0974
Polymers93,8642
Non-polymers1,2332
Water19,3661075
1
A: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5492
Polymers46,9321
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5492
Polymers46,9321
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.470, 55.900, 103.900
Angle α, β, γ (deg.)90.00, 118.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-686-

HOH

21B-691-

HOH

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Components

#1: Protein Dye-decolorizing peroxidase


Mass: 46932.074 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)
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: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1075 / 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: 1.071541 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: 1.071541 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 181153 / % possible obs: 99.3 % / Redundancy: 6.3 % / Net I/σ(I): 14.2
Reflection shellResolution: 1.4→1.49 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.972 / Mean I/σ(I) obs: 1.5 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AFV

4afv


Resolution: 1.401→42.987 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1839 9041 5 %
Rwork0.1442 --
obs0.1461 180986 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.401→42.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6580 0 86 1075 7741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046836
X-RAY DIFFRACTIONf_angle_d0.9929353
X-RAY DIFFRACTIONf_dihedral_angle_d13.4442399
X-RAY DIFFRACTIONf_chiral_restr0.0541042
X-RAY DIFFRACTIONf_plane_restr0.0051249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4013-1.41720.32822550.28144914X-RAY DIFFRACTION86
1.4172-1.43380.29022990.22415696X-RAY DIFFRACTION98
1.4338-1.45130.27592980.21295669X-RAY DIFFRACTION100
1.4513-1.46970.25443020.20285763X-RAY DIFFRACTION100
1.4697-1.4890.26323000.19215697X-RAY DIFFRACTION100
1.489-1.50940.26873040.18295763X-RAY DIFFRACTION100
1.5094-1.5310.24493010.1735721X-RAY DIFFRACTION100
1.531-1.55390.23153040.16695796X-RAY DIFFRACTION100
1.5539-1.57810.23073000.16445686X-RAY DIFFRACTION100
1.5781-1.6040.21633020.15815738X-RAY DIFFRACTION100
1.604-1.63170.22353020.14915728X-RAY DIFFRACTION100
1.6317-1.66140.21353030.14945745X-RAY DIFFRACTION100
1.6614-1.69330.19343030.14215767X-RAY DIFFRACTION100
1.6933-1.72790.19843000.13745709X-RAY DIFFRACTION100
1.7279-1.76540.23020.1335723X-RAY DIFFRACTION100
1.7654-1.80650.21993060.14045818X-RAY DIFFRACTION100
1.8065-1.85170.19893020.1365738X-RAY DIFFRACTION100
1.8517-1.90180.19183030.13565735X-RAY DIFFRACTION100
1.9018-1.95770.17153030.13465764X-RAY DIFFRACTION100
1.9577-2.02090.17663020.13385730X-RAY DIFFRACTION100
2.0209-2.09310.17573040.13235759X-RAY DIFFRACTION100
2.0931-2.17690.17843040.12985803X-RAY DIFFRACTION100
2.1769-2.2760.17393020.1315739X-RAY DIFFRACTION100
2.276-2.3960.17333040.12955786X-RAY DIFFRACTION100
2.396-2.54610.17813040.12625794X-RAY DIFFRACTION100
2.5461-2.74270.16323060.1345794X-RAY DIFFRACTION100
2.7427-3.01860.17583030.14485763X-RAY DIFFRACTION100
3.0186-3.45520.17513070.15265829X-RAY DIFFRACTION100
3.4552-4.35260.15933050.13385844X-RAY DIFFRACTION100
4.3526-43.00690.15713110.15085934X-RAY DIFFRACTION99

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