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- PDB-7qze: SFX structure of dye-type peroxidase DtpB D152A variant in the fe... -

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Basic information

Entry
Database: PDB / ID: 7qze
TitleSFX structure of dye-type peroxidase DtpB D152A variant in the ferryl state
ComponentsDyp-type peroxidase family
KeywordsOXIDOREDUCTASE / haem / peroxidase / ferric
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 / Dyp-type peroxidase family
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLucic, M. / Worrall, J.A.R. / Hough, M.A. / Shilova, A. / Axford, D.A. / Owen, R.L. / Tosha, T. / Sugimoto, H. / Owada, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R021015/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2022
Title: Serial Femtosecond Crystallography Reveals the Role of Water in the One- or Two-Electron Redox Chemistry of Compound I in the Catalytic Cycle of the B-Type Dye-Decolorizing Peroxidase DtpB.
Authors: Lucic, M. / Wilson, M.T. / Tosha, T. / Sugimoto, H. / Shilova, A. / Axford, D. / Owen, R.L. / Hough, M.A. / Worrall, J.A.R.
History
DepositionJan 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dyp-type peroxidase family
B: Dyp-type peroxidase family
C: Dyp-type peroxidase family
D: Dyp-type peroxidase family
E: Dyp-type peroxidase family
F: Dyp-type peroxidase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,63721
Polymers204,7696
Non-polymers3,86815
Water14,826823
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23310 Å2
ΔGint-232 kcal/mol
Surface area67130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.520, 120.900, 197.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Dyp-type peroxidase family


Mass: 34128.211 Da / Num. of mol.: 6 / Mutation: D152A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: SSPG_00656 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U8UU09
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 823 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: 6.2 mg/mL of protein in 20mM Sodium phosphate, 125mM NaCl pH 7 mixed with 125 mM MgCl2, 125 mM HEPES, 18% 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: 1.127 Å
DetectorType: MPCCD / Detector: CCD / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.9→36 Å / Num. obs: 163211 / % possible obs: 100 % / Redundancy: 1510 % / CC1/2: 0.968 / R split: 0.162 / Net I/σ(I): 4.8
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 16133 / CC1/2: 0.282 / R split: 0.863
Serial crystallography measurementPulse duration: 10 fsec.
Serial crystallography sample deliveryDescription: high-viscosity cartridge-type injector / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: hydroxyethyl cellulose / Flow rate: 0.0068 µL/min / Injector diameter: 100 µm / Power by: gas

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
CrystFEL0.10.00data reduction
CrystFEL0.10.00data scaling
REFMAC5.8.0267phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YRJ

6yrj


Resolution: 1.9→36 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.631 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 8066 4.9 %RANDOM
Rwork0.1662 ---
obs0.1679 155135 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.24 Å2 / Biso mean: 29.268 Å2 / Biso min: 16.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 1.9→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13904 0 267 823 14994
Biso mean--24.89 35.28 -
Num. residues----1835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01314615
X-RAY DIFFRACTIONr_bond_other_d0.0010.01413476
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.67719962
X-RAY DIFFRACTIONr_angle_other_deg1.3751.59230945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6851853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.56620.561784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.352152185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.17815137
X-RAY DIFFRACTIONr_chiral_restr0.0720.21853
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216859
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023451
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 589 -
Rwork0.317 11340 -
all-11929 -
obs--99.98 %

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