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- PDB-9fbj: Dye-decolourising peroxidase DtpB XRPP experiment (500 kGy) -

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Basic information

Entry
Database: PDB / ID: 9fbj
TitleDye-decolourising peroxidase DtpB XRPP experiment (500 kGy)
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: 1.9 Å
AuthorsLucic, M. / Worrall, J.A.R. / Hough, M.A. / Owen, R.L. / Maly, M.
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 XRPP experiment (500 kGy)
Authors: Lucic, M. / Worrall, J.A.R. / Hough, M.A. / Owen, R.L. / Maly, M.
History
DepositionMay 14, 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)206,87717
Polymers203,0816
Non-polymers3,79611
Water12,701705
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23020 Å2
ΔGint-250 kcal/mol
Surface area68820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.070, 122.745, 199.978
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.: 3 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / 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: 53.38 %
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: SACLA / Beamline: BL2 / Wavelength: 1.1263 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: 1.1263 Å / Relative weight: 1
ReflectionResolution: 1.9→34.97 Å / Num. obs: 168768 / % possible obs: 100 % / Redundancy: 57.3 % / CC1/2: 0.986 / R split: 0.268 / Net I/σ(I): 6.4
Reflection shellResolution: 1.9→1.949 Å / Redundancy: 56.8 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 11738 / CC1/2: 0.35 / R split: 1.395
Serial crystallography measurementPulse duration: 10 fsec. / Pulse energy: 358 µJ / 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: 6831

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→34.97 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.957 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27242 8457 5 %RANDOM
Rwork0.22398 ---
obs0.22641 160251 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.696 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0 Å2
2--0.6 Å2-0 Å2
3----0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.9→34.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13923 0 263 705 14891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01214732
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613519
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.85520112
X-RAY DIFFRACTIONr_angle_other_deg0.7611.76131055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11451869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.8575143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.914102215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1090.22190
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217978
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023498
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_it3.1772.3677422
X-RAY DIFFRACTIONr_mcbond_other3.1752.3687422
X-RAY DIFFRACTIONr_mcangle_it4.4454.2529300
X-RAY DIFFRACTIONr_mcangle_other4.4454.2529301
X-RAY DIFFRACTIONr_scbond_it3.6622.6887310
X-RAY DIFFRACTIONr_scbond_other3.6622.6887304
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4574.78510810
X-RAY DIFFRACTIONr_long_range_B_refined6.97121.8515327
X-RAY DIFFRACTIONr_long_range_B_other6.96921.8515313
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
Rfree0.369 614 -
Rwork0.327 11738 -
obs--99.99 %

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