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- PDB-9fbc: Dye-decolourising peroxidase DtpB (448 kGy) -

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Basic information

Entry
Database: PDB / ID: 9fbc
TitleDye-decolourising peroxidase DtpB (448 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 / Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
Similarity search - Component
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 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 (448 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

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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)206,78012
Polymers203,0816
Non-polymers3,6996
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22330 Å2
ΔGint-235 kcal/mol
Surface area65660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.984, 121.963, 199.607
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.62 Å3/Da / Density % sol: 52.96 %
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: Y
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: 2.72→40.16 Å / Num. obs: 57840 / % possible obs: 100 % / Redundancy: 140.5 % / CC1/2: 0.9925 / R split: 0.115 / Net I/σ(I): 1.2
Reflection shellResolution: 2.72→2.79 Å / Mean I/σ(I) obs: 0.47 / Num. unique obs: 3934 / CC1/2: 0.52 / R split: 0.782
Serial crystallography measurementPulse energy: 2.05E-9 µJ / Source size: 64 µm2
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetCrystals per unit: 25600 / Sample dehydration prevention: mylar / Sample holding: silicone chip
Serial crystallography data reductionCrystal hits: 16846

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→40.16 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.867 / SU B: 33.47 / SU ML: 0.62 / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28625 2931 5.1 %RANDOM
Rwork0.23496 ---
obs0.23753 54838 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0 Å2
2---0.33 Å20 Å2
3---0.22 Å2
Refinement stepCycle: 1 / Resolution: 2.72→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13766 0 258 2 14026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01214366
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613092
X-RAY DIFFRACTIONr_angle_refined_deg2.6921.8519618
X-RAY DIFFRACTIONr_angle_other_deg0.8831.75130146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.99551827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.6725113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.676102120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.22164
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217287
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023313
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_it7.975.5727326
X-RAY DIFFRACTIONr_mcbond_other7.975.5727326
X-RAY DIFFRACTIONr_mcangle_it11.55210.0029147
X-RAY DIFFRACTIONr_mcangle_other11.55110.0039148
X-RAY DIFFRACTIONr_scbond_it8.6025.9057040
X-RAY DIFFRACTIONr_scbond_other8.6025.9057039
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.45310.6810472
X-RAY DIFFRACTIONr_long_range_B_refined14.68749.9714881
X-RAY DIFFRACTIONr_long_range_B_other14.68649.9714882
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.72→2.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 239 -
Rwork0.396 3934 -
obs--99.64 %

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