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- PDB-4w7m: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICUL... -

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Basic information

Entry
Database: PDB / ID: 4w7m
TitleCRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. W377S MUTANT
ComponentsDye-decolorizing peroxidase
KeywordsOXIDOREDUCTASE / HEME / GLYCOPROTEIN
Function / homology
Function and homology information


dye decolorizing peroxidase / lactoperoxidase activity / peroxidase / peroxidase activity / heme binding / extracellular region / metal ion binding
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 (ear fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,2494
Polymers94,0162
Non-polymers1,2332
Water24,2301345
1
A: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6252
Polymers47,0081
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6252
Polymers47,0081
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.960, 56.170, 104.120
Angle α, β, γ (deg.)90.00, 118.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dye-decolorizing peroxidase


Mass: 47008.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Auricularia auricula-judae (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 / Heme B


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


Mass: 18.015 Da / Num. of mol.: 1345 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 32.5% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.005822 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: 1.005822 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 319222 / % possible obs: 95.1 % / Redundancy: 5.9 % / Net I/σ(I): 13.1
Reflection shellResolution: 1.15→1.22 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.3 / % possible all: 72.1

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Processing

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

4afv


Resolution: 1.15→41.249 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1499 15932 4.99 %
Rwork0.1313 --
obs0.1322 319118 95.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.15→41.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6592 0 86 1345 8023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076921
X-RAY DIFFRACTIONf_angle_d1.39467
X-RAY DIFFRACTIONf_dihedral_angle_d13.6982445
X-RAY DIFFRACTIONf_chiral_restr0.0741050
X-RAY DIFFRACTIONf_plane_restr0.0081260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1464-1.15950.23752580.2034963X-RAY DIFFRACTION47
1.1595-1.17310.20383790.1827125X-RAY DIFFRACTION68
1.1731-1.18740.20034040.17927960X-RAY DIFFRACTION75
1.1874-1.20250.20164500.17518778X-RAY DIFFRACTION83
1.2025-1.21830.2115040.16149563X-RAY DIFFRACTION90
1.2183-1.2350.19615300.15910131X-RAY DIFFRACTION96
1.235-1.25260.18285560.149110541X-RAY DIFFRACTION100
1.2526-1.27130.17795560.146910561X-RAY DIFFRACTION100
1.2713-1.29120.18255530.143310487X-RAY DIFFRACTION100
1.2912-1.31230.17795600.13710644X-RAY DIFFRACTION100
1.3123-1.3350.16535560.132210572X-RAY DIFFRACTION100
1.335-1.35930.15965550.125710546X-RAY DIFFRACTION100
1.3593-1.38540.14545580.122310586X-RAY DIFFRACTION100
1.3854-1.41370.15335570.12110569X-RAY DIFFRACTION100
1.4137-1.44440.13955560.11610601X-RAY DIFFRACTION100
1.4444-1.4780.14885580.117110588X-RAY DIFFRACTION100
1.478-1.5150.14225560.114510559X-RAY DIFFRACTION100
1.515-1.55590.14695580.113610629X-RAY DIFFRACTION100
1.5559-1.60170.14525580.112110599X-RAY DIFFRACTION100
1.6017-1.65340.14025570.112510577X-RAY DIFFRACTION100
1.6534-1.71250.13925570.116110600X-RAY DIFFRACTION100
1.7125-1.78110.14165600.120610623X-RAY DIFFRACTION100
1.7811-1.86220.14635570.123510567X-RAY DIFFRACTION100
1.8622-1.96030.15185590.125910642X-RAY DIFFRACTION100
1.9603-2.08310.13965590.125310631X-RAY DIFFRACTION100
2.0831-2.2440.13985620.124310665X-RAY DIFFRACTION100
2.244-2.46980.14665610.126210633X-RAY DIFFRACTION100
2.4698-2.82710.13895630.136310694X-RAY DIFFRACTION100
2.8271-3.56150.16775640.147110708X-RAY DIFFRACTION100
3.5615-41.27580.12835710.133310844X-RAY DIFFRACTION99

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