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- PDB-6fsl: F194W mutant of the dye-decolorizing peroxidase (DYP) from Pleuro... -

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Basic information

Entry
Database: PDB / ID: 6fsl
TitleF194W mutant of the dye-decolorizing peroxidase (DYP) from Pleurotus ostreatus
ComponentsDyP-type peroxidase
KeywordsOXIDOREDUCTASE
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 family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / DyP-type peroxidase
Similarity search - Component
Biological speciesPleurotus ostreatus (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRomero, A. / Davo-Siguero, I.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-77835-R Spain
CitationJournal: To Be Published
Title: Structure of two mutants: F194Y and F194W of the Dye-decolorizing peroxidase DYP from Pleurotus ostreatus
Authors: Romero, A. / Davo-Siguero, I. / Martinez, A.T.
History
DepositionFeb 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: DyP-type peroxidase
B: DyP-type peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4764
Polymers106,2432
Non-polymers1,2332
Water3,315184
1
A: DyP-type peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7382
Polymers53,1221
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DyP-type peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7382
Polymers53,1221
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.869, 118.140, 133.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DyP-type peroxidase


Mass: 53121.629 Da / Num. of mol.: 2 / Mutation: F194W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurotus ostreatus (oyster mushroom) / Gene: DyP4, PLEOSDRAFT_1069077 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A067N4E7
#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.: 184 / 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: 2.21 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.75 / Details: 0.2M MES pH=5.75 25% PEG2000 MME

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976252 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationMonochromator: Standard ESRF channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976252 Å / Relative weight: 1
ReflectionResolution: 2.5→88.35 Å / Num. obs: 34465 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 31.427 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.268 / Rpim(I) all: 0.167 / Net I/σ(I): 7.7
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.923 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4873 / CC1/2: 0.757 / Rpim(I) all: 0.57 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AFV

3afv


Resolution: 2.5→88.35 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.889 / SU B: 10.318 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.991 / ESU R Free: 0.301 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24317 1667 4.8 %RANDOM
Rwork0.18052 ---
obs0.1836 32741 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.894 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å2-0 Å2
2---0.93 Å20 Å2
3---0.83 Å2
Refinement stepCycle: 1 / Resolution: 2.5→88.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7496 0 86 184 7766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197802
X-RAY DIFFRACTIONr_bond_other_d0.0020.027306
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.96410613
X-RAY DIFFRACTIONr_angle_other_deg0.994316851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8115966
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22724.223367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.418151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.851546
X-RAY DIFFRACTIONr_chiral_restr0.0930.21114
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218984
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021838
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_it1.6872.4223870
X-RAY DIFFRACTIONr_mcbond_other1.6852.4223869
X-RAY DIFFRACTIONr_mcangle_it2.9043.6284834
X-RAY DIFFRACTIONr_mcangle_other2.9043.6294835
X-RAY DIFFRACTIONr_scbond_it1.6522.5093932
X-RAY DIFFRACTIONr_scbond_other1.6522.5093930
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8463.6945779
X-RAY DIFFRACTIONr_long_range_B_refined4.87927.5248378
X-RAY DIFFRACTIONr_long_range_B_other4.87627.5158368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 117 -
Rwork0.222 2308 -
obs--95.74 %

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