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- PDB-9fbz: Dye-decolourising peroxidase DtpB mixed with hydrogen peroxide fo... -

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Basic information

Entry
Database: PDB / ID: 9fbz
TitleDye-decolourising peroxidase DtpB mixed with hydrogen peroxide for 1.3 s
ComponentsPutative dye-decolorizing peroxidase (DyP), encapsulated subgroup
KeywordsOXIDOREDUCTASE / Dye-decolourising peroxidase / heme peroxidase
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: 1.96 Å
AuthorsLucic, M. / Worrall, J.A.R. / Hough, M.A. / Owen, R.L. / Devenish, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Dye-decolourising peroxidase DtpB mixed with hydrogen peroxide for 1.3 s
Authors: Lucic, M. / Worrall, J.A.R. / Hough, M.A. / Owen, R.L. / Devenish, N.
History
DepositionMay 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: 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)206,89318
Polymers203,0816
Non-polymers3,81212
Water12,791710
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23240 Å2
ΔGint-250 kcal/mol
Surface area67880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.926, 121.697, 199.447
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 BL21(DE3) (bacteria) / 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.: 4 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: 6.2 mg/mL of protein in 20 mM NaPi, 150 mM NaCl pH 7 was mixed with 125 mM MgCl2, 125 mM HEPES, 18% 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: PAL-XFEL / Beamline: NCI / Wavelength: 1.3042 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jun 26, 2022 / Frequency: 30
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3042 Å / Relative weight: 1
ReflectionResolution: 1.96→35.28 Å / Num. obs: 152802 / % possible obs: 100 % / Redundancy: 165.8 % / CC1/2: 0.992 / Net I/σ(I): 12
Reflection shellResolution: 1.96→2.011 Å / Num. unique obs: 10534 / CC1/2: 0.23
Serial crystallography measurementPulse duration: 25 fsec. / Pulse photon energy: 9.5 keV
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: mylar / Sample holding: silicon chip
Serial crystallography data reductionCrystal hits: 23641

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→35.28 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.624 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19794 7546 5 %RANDOM
Rwork0.1674 ---
obs0.1689 144460 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.976 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0 Å20 Å2
2--0.13 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.96→35.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13922 0 264 710 14896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01214723
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613530
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.68420119
X-RAY DIFFRACTIONr_angle_other_deg0.5831.58731087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63151869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.7855142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.121102213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.22196
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217954
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023490
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_it4.4843.5937431
X-RAY DIFFRACTIONr_mcbond_other4.4793.5937431
X-RAY DIFFRACTIONr_mcangle_it5.8276.4499315
X-RAY DIFFRACTIONr_mcangle_other5.8266.459316
X-RAY DIFFRACTIONr_scbond_it5.574.0827292
X-RAY DIFFRACTIONr_scbond_other5.5714.0837290
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8417.26410804
X-RAY DIFFRACTIONr_long_range_B_refined10.12734.0715289
X-RAY DIFFRACTIONr_long_range_B_other10.12634.0715277
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.49 555 -
Rwork0.5 10534 -
obs--100 %

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