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- PDB-9f1q: Crystal structure of a DyP-type peroxidase Fireprot variant from ... -

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Basic information

Entry
Database: PDB / ID: 9f1q
TitleCrystal structure of a DyP-type peroxidase Fireprot variant from Pseudomonas putida
ComponentsDyp-type peroxidase family protein
KeywordsOXIDOREDUCTASE / Protein Stability / Protein Engineering / Computational Engineering / DyPs
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / 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 family protein
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLorena, C. / Borges, P.T. / Frazao, C. / Martins, L.O.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)EXPL/BIA-BQM/0473/2021 Portugal
Foundation for Science and Technology (FCT)2022.02027.PTDC Portugal
CitationJournal: Acs Catalysis / Year: 2025
Title: Network Dynamics as Fingerprints of Thermostability in an In Silico-Engineered DyP-Type Peroxidase.
Authors: Rodrigues, C.F. / Silva, D. / Lorena, C. / Borges, P.T. / Masgrau, L. / Martins, L.O.
History
DepositionApr 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 24, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dyp-type peroxidase family protein
B: Dyp-type peroxidase family protein
C: Dyp-type peroxidase family protein
D: Dyp-type peroxidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,26720
Polymers125,9224
Non-polymers3,34516
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16130 Å2
ΔGint-160 kcal/mol
Surface area42050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.949, 144.949, 177.158
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Dyp-type peroxidase family protein


Mass: 31480.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: PP_3248 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88HV5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.27 Å3/Da / Density % sol: 71.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.2 M sodium iodide, 0.1 M Bis-Tris propane pH 6.5 and 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.35→67.08 Å / Num. obs: 89670 / % possible obs: 99.9 % / Redundancy: 12.7 % / Rpim(I) all: 0.057 / Net I/σ(I): 9.29
Reflection shellResolution: 2.35→2.45 Å / Num. unique obs: 14296 / Rpim(I) all: 0.2919

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→59.16 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 1998 2.23 %
Rwork0.2189 --
obs0.2195 89630 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→59.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8879 0 224 392 9495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039350
X-RAY DIFFRACTIONf_angle_d0.63112747
X-RAY DIFFRACTIONf_dihedral_angle_d13.6283390
X-RAY DIFFRACTIONf_chiral_restr0.041321
X-RAY DIFFRACTIONf_plane_restr0.0051681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.43231370.38216150X-RAY DIFFRACTION99
2.41-2.470.37971410.33646155X-RAY DIFFRACTION100
2.47-2.550.36541440.2966225X-RAY DIFFRACTION100
2.55-2.630.31761390.27676196X-RAY DIFFRACTION100
2.63-2.720.31961460.27366215X-RAY DIFFRACTION100
2.72-2.830.30831400.25426213X-RAY DIFFRACTION100
2.83-2.960.27071460.2336213X-RAY DIFFRACTION100
2.96-3.120.23321420.20586220X-RAY DIFFRACTION100
3.12-3.310.24751420.20546264X-RAY DIFFRACTION100
3.31-3.570.22131410.19516267X-RAY DIFFRACTION100
3.57-3.930.19331430.18996284X-RAY DIFFRACTION100
3.93-4.50.23521430.17086309X-RAY DIFFRACTION100
4.5-5.660.1851420.19086344X-RAY DIFFRACTION100
5.67-59.160.2531520.24686577X-RAY DIFFRACTION100

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