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- PDB-3afv: Dye-decolorizing peroxidase (DyP) at 1.4 A resolution -

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Basic information

Entry
Database: PDB / ID: 3afv
TitleDye-decolorizing peroxidase (DyP) at 1.4 A resolution
ComponentsDyP
KeywordsOXIDOREDUCTASE / dyp / dye-decolorizing peroxidase / beta barrel / aspartic acid
Function / homology
Function and homology information


peroxidase activity / heme binding / 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 / DyP
Similarity search - Component
Biological speciesBjerkandera adusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSugano, Y. / Yoshida, T. / Tsuge, H.
CitationJournal: Febs J. / Year: 2011
Title: The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue
Authors: Yoshida, T. / Tsuge, H. / Konno, H. / Hisabori, T. / Sugano, Y.
History
DepositionMar 11, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 26, 2011Group: Database references / Source and taxonomy
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DyP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3353
Polymers47,4971
Non-polymers8382
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.789, 95.968, 50.303
Angle α, β, γ (deg.)90.00, 103.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DyP / dye-decolorizing peroxidase


Mass: 47497.344 Da / Num. of mol.: 1 / Fragment: residues in UNP 57-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bjerkandera adusta (fungus) / Plasmid: pTAex3 / Production host: Aspergillus oryzae (mold) / Strain (production host): M-2-3 / References: UniProt: Q8WZK8, dye decolorizing peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 15, 2009
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 83584 / % possible obs: 98.9 % / Observed criterion σ(I): 9.3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.073 / Rsym value: 0.058 / Χ2: 1.097 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.423.40.35739770.767193.8
1.42-1.453.50.3440390.757196.2
1.45-1.483.60.31441260.765198
1.48-1.513.60.30641860.801198.8
1.51-1.543.70.26541290.771198.8
1.54-1.583.70.2441610.805198.9
1.58-1.623.70.21542410.834199.3
1.62-1.663.70.19141240.825199.2
1.66-1.713.70.16941750.853199.3
1.71-1.763.80.14241730.859199.5
1.76-1.833.70.12142280.892199.6
1.83-1.93.80.09741780.91199.7
1.9-1.993.80.07942190.926199.8
1.99-2.093.80.06842101.021199.8
2.09-2.223.80.06142471.088199.9
2.22-2.393.80.05442211.1381100
2.39-2.633.80.05142211.2291100
2.63-3.023.80.04842251.4781100
3.02-3.83.70.04642382.058199.8
3.8-503.60.04942663.073198.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2d3q

2d3q


Resolution: 1.4→48.85 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.888 / SU B: 0.893 / SU ML: 0.036 / SU R Cruickshank DPI: 0.06 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4172 5 %random
Rwork0.178 79392 --
obs0.179 83564 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 33.23 Å2 / Biso mean: 10.553 Å2 / Biso min: 3.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å20.36 Å2
2---0.94 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 57 230 3625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223490
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9894777
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8465438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02124.908163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.91115495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4551516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212774
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6161.52183
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1423519
X-RAY DIFFRACTIONr_scbond_it1.68631307
X-RAY DIFFRACTIONr_scangle_it2.6234.51258
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 291 -
Rwork0.238 5372 -
all-5663 -
obs--91.22 %

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