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- PDB-9fb9: Dye-decolourising peroxidase DtpB (336 kGy) -

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Basic information

Entry
Database: PDB / ID: 9fb9
TitleDye-decolourising peroxidase DtpB (336 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 / Dye-decolorizing peroxidase (DyP), encapsulated subgroup
Similarity search - Component
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsLucic, M. / Worrall, J.A.R. / Hough, M.A. / Strange, R.W. / Owen, R.L.
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 (336 kGy)
Authors: Lucic, M. / Worrall, J.A.R. / Hough, M.A. / Strange, R.W. / Owen, R.L.
History
DepositionMay 13, 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)206,99814
Polymers203,0816
Non-polymers3,9178
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22350 Å2
ΔGint-240 kcal/mol
Surface area66390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.941, 121.947, 199.589
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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 293 K / Method: batch mode
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: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.19→40.14 Å / Num. obs: 109752 / % possible obs: 100 % / Redundancy: 95.4 % / CC1/2: 0.99 / R split: 0.132 / Net I/σ(I): 1.33
Reflection shellResolution: 2.19→2.247 Å / Mean I/σ(I) obs: 0.47 / Num. unique obs: 7619 / CC1/2: 0.53 / R split: 0.748
Serial crystallography measurementPulse energy: 2.05E-9 µJ / Source size: 64 µm2
Serial crystallography sample delivery fixed targetCrystals per unit: 25600 / Sample dehydration prevention: mylar / Sample holding: silicone chip
Serial crystallography data reductionCrystal hits: 19785

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→40.14 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.913 / SU B: 17.929 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27291 5471 5 %RANDOM
Rwork0.2468 ---
obs0.24811 104192 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.851 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.19→40.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13937 0 130 10 14077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01214407
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613167
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.8519666
X-RAY DIFFRACTIONr_angle_other_deg0.7381.75230317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.05751828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.0135115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.895102136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.22167
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217315
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023321
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_it3.6143.5547330
X-RAY DIFFRACTIONr_mcbond_other3.6143.5547330
X-RAY DIFFRACTIONr_mcangle_it5.5146.3689152
X-RAY DIFFRACTIONr_mcangle_other5.5146.3689153
X-RAY DIFFRACTIONr_scbond_it4.3993.8537077
X-RAY DIFFRACTIONr_scbond_other4.3993.8547076
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7636.92310515
X-RAY DIFFRACTIONr_long_range_B_refined8.53231.8915015
X-RAY DIFFRACTIONr_long_range_B_other8.53231.8915012
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 373 -
Rwork0.401 7619 -
obs--99.69 %

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