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- PDB-8pxp: Compound II structure of Y389F variant of A type dye-decolourisin... -

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Basic information

Entry
Database: PDB / ID: 8pxp
TitleCompound II structure of Y389F variant of A type dye-decolourising peroxidase DtpAa
ComponentsDeferrochelatase
KeywordsOXIDOREDUCTASE / Heme peroxidase / dye-decolourising peroxidase / Compound II
Function / homology
Function and homology information


iron import into cell / cell envelope / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / lyase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
Deferrochelatase / : / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN ATOM / Deferrochelatase
Similarity search - Component
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLucic, M. / Thompson, A. / 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: To Be Published
Title: Compound II structure of A type dye-decolourising peroxidase DtpAa
Authors: Lucic, M. / Thompson, A. / Worrall, J.A.R. / Hough, M.A.
History
DepositionJul 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deferrochelatase
B: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7326
Polymers88,4672
Non-polymers1,2654
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-60 kcal/mol
Surface area25310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.939, 67.543, 70.797
Angle α, β, γ (deg.)90.00, 104.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deferrochelatase / Peroxidase EfeB


Mass: 44233.418 Da / Num. of mol.: 2 / Mutation: Y389F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SLI_2602 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A7U9DT46, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7
Details: 1:1 v/v solutions of 6.2 mg/ Y389F DtpAa in 20 mM sodium phosphate, 150 mM NaCl pH 7 with a precipitant solution consisting of 100 mM HEPES pH 7, 20% 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: Sep 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.01→48.08 Å / Num. obs: 45274 / % possible obs: 99 % / Redundancy: 5.2 % / CC1/2: 0.958 / Rmerge(I) obs: 0.316 / Net I/σ(I): 8.9
Reflection shellResolution: 2.01→2.04 Å / Rmerge(I) obs: 1.174 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2256 / CC1/2: 0.368

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
DIALSdata reduction
xia2.multiplexdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→43.88 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.071 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2186 4.8 %RANDOM
Rwork0.21 ---
obs0.21003 45241 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.522 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0.48 Å2
2---0.53 Å2-0 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.01→43.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 2 303 5867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.765
X-RAY DIFFRACTIONf_dihedral_angle_d15.0542015
X-RAY DIFFRACTIONf_chiral_restr0.044820
X-RAY DIFFRACTIONf_plane_restr0.0091039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.050.28381420.22372679X-RAY DIFFRACTION100
2.05-2.10.30631580.2292678X-RAY DIFFRACTION100
2.1-2.150.26951570.21982681X-RAY DIFFRACTION100
2.15-2.210.29441230.21182714X-RAY DIFFRACTION100
2.21-2.280.30441390.21112694X-RAY DIFFRACTION100
2.28-2.350.27741420.21182684X-RAY DIFFRACTION99
2.35-2.430.2861220.22122684X-RAY DIFFRACTION100
2.43-2.530.26431420.20972687X-RAY DIFFRACTION99
2.53-2.650.27491430.2222647X-RAY DIFFRACTION98
2.65-2.790.25651270.20762678X-RAY DIFFRACTION98
2.79-2.960.28191520.20892702X-RAY DIFFRACTION100
2.96-3.190.28911130.22042704X-RAY DIFFRACTION99
3.19-3.510.25781210.21112720X-RAY DIFFRACTION99
3.51-4.020.25421370.20732718X-RAY DIFFRACTION99
4.02-5.060.19991210.18922719X-RAY DIFFRACTION98
5.06-43.840.20841470.19452666X-RAY DIFFRACTION96

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