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- PDB-5ikd: Asymmetric sulfoxidation by engineering the heme pocket of a dye-... -

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Basic information

Entry
Database: PDB / ID: 5ikd
TitleAsymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase
ComponentsDye-decolorizing peroxidase
KeywordsOXIDOREDUCTASE / DECOLORIZING PEROXIDASE (DYP) / F359G VARIANT / HEME
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 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: 1.109 Å
AuthorsRomero, A. / Davo-Siguero, I. / Martinez, A.T.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-55448-P Spain
Citation
Journal: Catalysis Science And Technology / Year: 2016
Title: Asymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase
Authors: Linde, D. / Canellas, M. / Davo-Siguero, I. / Romero, A. / Lucas, F. / Ruiz-Duenas, F.J. / Guallar, V. / Martinez, A.T.
#1: Journal: Biochem. J. / Year: 2015
Title: Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study.
Authors: 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
DepositionMar 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
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 / _pdbx_audit_support.funding_organization
Revision 3.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3302
Polymers46,7141
Non-polymers6161
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-18 kcal/mol
Surface area16330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.928, 56.065, 82.709
Angle α, β, γ (deg.)90.000, 97.030, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1098-

HOH

21A-1171-

HOH

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Components

#1: Protein Dye-decolorizing peroxidase


Mass: 46713.805 Da / Num. of mol.: 1 / Fragment: UNP residues 64-509 / Mutation: F359G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Auricularia auricula-judae (jelly 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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 2M magnesium formate and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.109→46.63 Å / Num. obs: 184770 / % possible obs: 98.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 9.14 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.11-1.175.10.753196.4
3.51-46.635.50.059199.5

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W7J

4w7j


Resolution: 1.109→41.261 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.48
RfactorNum. reflection% reflection
Rfree0.1581 1897 1.03 %
Rwork0.1495 --
obs0.1496 184736 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.87 Å2 / Biso mean: 14.0754 Å2 / Biso min: 5.01 Å2
Refinement stepCycle: final / Resolution: 1.109→41.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 73 576 3947
Biso mean--8.62 24.72 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063437
X-RAY DIFFRACTIONf_angle_d0.9874703
X-RAY DIFFRACTIONf_chiral_restr0.079521
X-RAY DIFFRACTIONf_plane_restr0.008627
X-RAY DIFFRACTIONf_dihedral_angle_d15.7141208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1089-1.13660.24611460.2301126911283796
1.1366-1.16740.21881340.202128091294396
1.1674-1.20170.18831490.1855127441289397
1.2017-1.24050.16781290.1796129031303297
1.2405-1.28490.16821190.1641128461296597
1.2849-1.33630.14271320.1532130431317598
1.3363-1.39710.16591390.1461130111315098
1.3971-1.47080.17291300.1377131011323199
1.4708-1.56290.1471340.1295132041333899
1.5629-1.68360.14221190.1313131591327899
1.6836-1.8530.14721400.141132701341099
1.853-2.12120.15291400.1464132621340299
2.1212-2.67240.14761520.14991332913481100
2.6724-41.28920.15321340.142134671360199

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