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- PDB-9qqy: Dye-decolourising peroxidase DtpB XRPP experiment (1000 kGy)-PUMP -

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Basic information

Entry
Database: PDB / ID: 9qqy
TitleDye-decolourising peroxidase DtpB XRPP experiment (1000 kGy)-PUMP
ComponentsPutative dye-decolorizing peroxidase (DyP), encapsulated subgroup
KeywordsOXIDOREDUCTASE / Heme peroxidase / Dye-decolourising peroxidase / XFEL / XRPP
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, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN ATOM / Dye-decolorizing peroxidase (DyP), encapsulated subgroup
Similarity search - Component
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLucic, M. / Worrall, J.A.R. / Hough, M.A. / Maly, M. / Owen, R.L.
Funding support1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)
CitationJournal: To Be Published
Title: Dye-decolourising peroxidase DtpB XRPP experiment (1000 kGy)-PUMP
Authors: Lucic, M. / Worrall, J.A.R. / Hough, M.A. / Maly, M. / Owen, R.L.
History
DepositionApr 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
B: Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
C: Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
D: Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
E: Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
F: Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,90919
Polymers203,0816
Non-polymers3,82813
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.054, 122.576, 200.237
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
Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup


Mass: 33846.836 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SLI_7409 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9HFU5
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7.5
Details: 6.2 mg/mL of protein in 20mM Sodium phosphate, 150mM NaCl pH 7 was mixed with 125 mM MgCl2, 125 mM HEPES, 20% PEG 4000 pH 7.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.1264 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1264 Å / Relative weight: 1
ReflectionResolution: 1.9→46.05 Å / Num. obs: 168749 / % possible obs: 100 % / Redundancy: 94.8 % / CC1/2: 0.914 / R split: 0.217 / Net I/σ(I): 5.9
Reflection shellResolution: 1.9→1.949 Å / Num. unique obs: 11732 / CC1/2: 0.25 / R split: 1.612
Serial crystallography measurementPulse duration: 10 fsec. / Pulse photon energy: 11 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: mylar / Sample holding: silicon chip
Serial crystallography data reductionCrystal hits: 11890

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→41.05 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.082 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26108 8458 5 %RANDOM
Rwork0.21506 ---
obs0.21737 160314 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.837 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2--0.22 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.9→41.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13923 0 265 648 14836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01214653
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613354
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.85519998
X-RAY DIFFRACTIONr_angle_other_deg0.6951.74630727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09451855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.9135198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.278102197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.22183
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023399
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_it3.352.7587387
X-RAY DIFFRACTIONr_mcbond_other3.3492.7587387
X-RAY DIFFRACTIONr_mcangle_it4.6434.9529244
X-RAY DIFFRACTIONr_mcangle_other4.6434.9539245
X-RAY DIFFRACTIONr_scbond_it4.0893.1377266
X-RAY DIFFRACTIONr_scbond_other4.0883.1377260
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1265.58210752
X-RAY DIFFRACTIONr_long_range_B_refined7.56325.2515246
X-RAY DIFFRACTIONr_long_range_B_other7.5625.2415234
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 615 -
Rwork0.351 11732 -
obs--100 %

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