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- PDB-6fsk: F194Y mutant of the Dye-decolorizing peroxidase (DYP) from Pleuro... -

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Basic information

Entry
Database: PDB / ID: 6fsk
TitleF194Y mutant of the Dye-decolorizing peroxidase (DYP) from Pleurotus ostreatus
ComponentsDyP-type peroxidaseDye decolorizing peroxidase
KeywordsOXIDOREDUCTASE
Function / homologyDyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel / peroxidase activity / heme binding / PROTOPORPHYRIN IX CONTAINING FE / DyP-type peroxidase
Function and homology information
Biological speciesPleurotus ostreatus PC15 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsRomero, A. / Davo-Siguero, I.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-77835-R Spain
CitationJournal: Acs Catalysis / Year: 2018
Title: Description of a non-canonical Mn(II)-oxidation site in peroxidases
Authors: Fernandez-Fueyo, E. / Davo-Siguero, I. / Almendral, D. / Linde, D. / Baratto, M.C. / Pogni, R. / Romero, A. / Guallar, V. / Martinez, A.T.
History
DepositionFeb 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 2.0Jan 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_data_processing_status ...atom_site / pdbx_data_processing_status / pdbx_nonpoly_scheme / pdbx_solvent_atom_site_mapping / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_solvent_atom_site_mapping.auth_seq_id
Revision 2.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id

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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)107,7055
Polymers106,2772
Non-polymers1,4283
Water20,1591119
1
A: DyP-type peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9503
Polymers53,1391
Non-polymers8122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DyP-type peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7552
Polymers53,1391
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.717, 117.575, 140.434
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 / Dye decolorizing peroxidase


Mass: 53138.641 Da / Num. of mol.: 2 / Mutation: F194Y
Source method: isolated from a genetically manipulated source
Details: Cysteine at position 147 is oxidized to S-hydroxycysteine
Source: (gene. exp.) Pleurotus ostreatus PC15 (fungus) / Gene: DyP4, PLEOSDRAFT_1069077 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: A0A067N4E7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1119 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.75 / Details: 0.2M MES pH=5.75 25%PEG 2000 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: 1.56→70.22 Å / Num. obs: 144926 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 17.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.051 / Rrim(I) all: 0.083 / Net I/σ(I): 12.7
Reflection shellResolution: 1.56→1.64 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 20996 / CC1/2: 0.745 / Rpim(I) all: 0.392 / Rrim(I) all: 0.649 / % possible all: 97.4

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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: 1.56→70.22 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.493 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19885 7250 5 %RANDOM
Rwork0.16201 ---
obs0.16386 137552 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.04 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.56→70.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7477 0 98 1119 8694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0197733
X-RAY DIFFRACTIONr_bond_other_d0.0020.027232
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.96610516
X-RAY DIFFRACTIONr_angle_other_deg1.237316681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1845955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03524.038364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.166151197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2371548
X-RAY DIFFRACTIONr_chiral_restr0.1330.21105
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0218883
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021827
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_it1.6641.6183829
X-RAY DIFFRACTIONr_mcbond_other1.6641.6183828
X-RAY DIFFRACTIONr_mcangle_it2.4122.4244781
X-RAY DIFFRACTIONr_mcangle_other2.4122.4244782
X-RAY DIFFRACTIONr_scbond_it2.761.8423904
X-RAY DIFFRACTIONr_scbond_other2.761.8423904
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1662.6575736
X-RAY DIFFRACTIONr_long_range_B_refined5.48820.8848995
X-RAY DIFFRACTIONr_long_range_B_other5.48820.8868996
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.556→1.597 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 553 -
Rwork0.307 10100 -
obs--97.39 %

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