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- PDB-6yrd: SFX structure of dye-type peroxidase DtpB in the ferryl state -

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Basic information

Entry
Database: PDB / ID: 6yrd
TitleSFX structure of dye-type peroxidase DtpB in the ferryl state
ComponentsPutative iron-dependent peroxidase
KeywordsOXIDOREDUCTASE / peroxidase / dye-decolourising / serial femtosecond crystallography / damage-free / ferryl
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLucic, M. / Axford, D.A. / Owen, R.L. / 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
Citation
Journal: 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.
#1: Journal: 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 FeIV=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 20, 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

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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
Water15,853880
1
A: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8294
Polymers34,1721
Non-polymers6573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8053
Polymers34,1721
Non-polymers6322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8294
Polymers34,1721
Non-polymers6573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9994
Polymers34,1721
Non-polymers8273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8053
Polymers34,1721
Non-polymers6322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8053
Polymers34,1721
Non-polymers6322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.300, 120.000, 198.450
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 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1H2DDB9

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Non-polymers , 5 types, 895 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.: 880 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 50.92 % / Description: Microcrystals
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: 6-10 mg/mL of protein in 50mM Sodium acetate, 150mM NaCl pH 5 was mixed with 150 mM MgCl2, 150 mM HEPES, 20% PEG 4000 pH 7.5

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Data collection

DiffractionMean temperature: 301 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.13 Å
DetectorType: MPCCD / Detector: CCD / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 1.75→102 Å / Num. obs: 207440 / % possible obs: 100 % / Redundancy: 1943 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.984 / R split: 0.109 / Net I/σ(I): 6.1
Reflection shellResolution: 1.75→1.8 Å / Num. unique obs: 10274 / CC1/2: 0.423 / R split: 0.887
Serial crystallography measurementPulse duration: 10 fsec. / Pulse energy: 156 µJ / Pulse photon energy: 11 keV
Serial crystallography sample deliveryDescription: silicon chip / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: silicon chip / Details: 25600 apertures per chip

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished structure

Resolution: 1.75→13 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.594 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1004 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.099
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1988 10353 5 %RANDOM
Rwork0.1666 ---
obs0.1682 196370 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.34 Å2 / Biso mean: 33.628 Å2 / Biso min: 19.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.75→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13904 0 279 880 15063
Biso mean--28.35 43.35 -
Num. residues----1830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01314905
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713639
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.67620396
X-RAY DIFFRACTIONr_angle_other_deg1.4451.59231428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77151910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.31920.69812
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.019152243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.36115141
X-RAY DIFFRACTIONr_chiral_restr0.0730.21881
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217404
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023451
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 767 -
Rwork0.363 14176 -
all-14943 -
obs--99.89 %

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