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- PDB-6yr4: Dye-type peroxidase DtpB in the ferryl state: Spectroscopically V... -

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Basic information

Entry
Database: PDB / ID: 6yr4
TitleDye-type peroxidase DtpB in the ferryl state: Spectroscopically Validated composite structure
ComponentsPutative iron-dependent peroxidase
KeywordsOXIDOREDUCTASE / peroxidase / dye-decolourising / spectroscopically-validated / DtpB
Function / homology
Function and homology information


peroxidase activity / heme binding
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 / Putative iron-dependent peroxidase
Similarity search - Component
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLucic, M. / Dworkowski, F.S.N. / Worrall, J.A.R. / Hough, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R021015/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe IV =O Formation.
Authors: Lucic, M. / Svistunenko, D.A. / Wilson, M.T. / Chaplin, A.K. / Davy, B. / Ebrahim, A. / Axford, D. / Tosha, T. / Sugimoto, H. / Owada, S. / Dworkowski, F.S.N. / Tews, I. / Owen, R.L. / ...Authors: Lucic, M. / Svistunenko, D.A. / Wilson, M.T. / Chaplin, A.K. / Davy, B. / Ebrahim, A. / Axford, D. / Tosha, T. / Sugimoto, H. / Owada, S. / Dworkowski, F.S.N. / Tews, I. / Owen, R.L. / Hough, M.A. / Worrall, J.A.R.
History
DepositionApr 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Feb 11, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative iron-dependent peroxidase
B: Putative iron-dependent peroxidase
C: Putative iron-dependent peroxidase
D: Putative iron-dependent peroxidase
E: Putative iron-dependent peroxidase
F: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,07121
Polymers205,0336
Non-polymers4,03815
Water21,5281195
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22950 Å2
ΔGint-231 kcal/mol
Surface area65310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.350, 119.910, 194.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 iron-dependent peroxidase


Mass: 34172.223 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SAMN05428941_7146 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1H2DDB9

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Non-polymers , 5 types, 1210 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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.: 6 / 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.: 1195 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: 6-10 mg/mL of protein in 50mM Sodium acteate, 150mM NaCl pH 5 mixed with 100 mM MgCl2, 100 mM HEPES pH 7.5, 16% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.85→48 Å / Num. obs: 159520 / % possible obs: 94.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 22.2 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.179 / Net I/σ(I): 4.4
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 12846 / CC1/2: 0.51 / % possible all: 79.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Refined from ferric SFX structure

Resolution: 1.85→47.61 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.175 / SU ML: 0.12 / SU R Cruickshank DPI: 0.1497 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.142
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 7982 5 %RANDOM
Rwork0.1882 ---
obs0.1903 151470 93.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.89 Å2 / Biso mean: 25.278 Å2 / Biso min: 14.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.65 Å20 Å2
3---0.73 Å2
Refinement stepCycle: final / Resolution: 1.85→47.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13855 0 279 1195 15329
Biso mean--21.19 32.21 -
Num. residues----1832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01314539
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713280
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.67819847
X-RAY DIFFRACTIONr_angle_other_deg1.3591.59130579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30651842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.78820.882771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.781152150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.86515128
X-RAY DIFFRACTIONr_chiral_restr0.0680.21845
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216789
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023311
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 510 -
Rwork0.29 9552 -
all-10062 -
obs--80.62 %

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