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- PDB-9ewi: Dye-decolourising peroxidase DtpB (168 kGy) -

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Basic information

Entry
Database: PDB / ID: 9ewi
TitleDye-decolourising peroxidase DtpB (168 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsLucic, M. / Worrall, J.A.R. / Hough, M.A. / Owen, R.L. / Strange, R.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R021015/1 United Kingdom
CitationJournal: To Be Published
Title: Dye-decolourising peroxidase DtpB (168 kGy)
Authors: Lucic, M. / Worrall, J.A.R. / Hough, M.A. / Owen, R.L. / Strange, R.W.
History
DepositionApr 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 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)206,56419
Polymers202,5596
Non-polymers4,00613
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23180 Å2
ΔGint-237 kcal/mol
Surface area66610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.812, 121.858, 199.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup


Mass: 33759.758 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

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Non-polymers , 5 types, 354 molecules

#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: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.39 %
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: 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: 1.83→40.09 Å / Num. obs: 186481 / % possible obs: 100 % / Redundancy: 70.7 % / CC1/2: 0.98 / R split: 0.13 / Net I/σ(I): 1.96
Reflection shellResolution: 1.83→1.88 Å / Num. unique obs: 12994 / CC1/2: 0.55 / R split: 0.736
Serial crystallography measurementPulse energy: 2.05E-9 µJ / Source size: 64 µm2
Serial crystallography sample deliveryDescription: silicone chip / Method: fixed target
Serial crystallography sample delivery fixed targetCrystals per unit: 25600 / Sample dehydration prevention: mylar / Sample holding: silicone chip
Serial crystallography data reductionCrystal hits: 22404

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→40.09 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.529 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23604 9188 4.9 %RANDOM
Rwork0.2036 ---
obs0.20518 177187 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: 31.653 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.83→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14044 0 87 341 14472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01214475
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613269
X-RAY DIFFRACTIONr_angle_refined_deg2.1761.85319754
X-RAY DIFFRACTIONr_angle_other_deg0.7881.75530525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08951830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.8365125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.177102159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.22169
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217453
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023371
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_it3.5352.9357332
X-RAY DIFFRACTIONr_mcbond_other3.5352.9357332
X-RAY DIFFRACTIONr_mcangle_it5.2565.2569155
X-RAY DIFFRACTIONr_mcangle_other5.2565.2579156
X-RAY DIFFRACTIONr_scbond_it5.0423.3667143
X-RAY DIFFRACTIONr_scbond_other5.0423.3667142
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4475.95610599
X-RAY DIFFRACTIONr_long_range_B_refined8.4326.8215332
X-RAY DIFFRACTIONr_long_range_B_other8.43226.7915306
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 652 -
Rwork0.386 12994 -
obs--99.82 %

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