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- PDB-8pxq: SFX Ferric structure of Y389F variant of A type dye-decolourising... -

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Basic information

Entry
Database: PDB / ID: 8pxq
TitleSFX Ferric structure of Y389F variant of A type dye-decolourising peroxidase DtpAa
ComponentsDeferrochelatase
KeywordsOXIDOREDUCTASE / Heme peroxidase / dye-decolourising peroxidase / ferric
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 / Deferrochelatase
Similarity search - Component
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLucic, M. / Worrall, J.A.R. / Hough, M.A. / Pfalzgraf, H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R021015/1 United Kingdom
CitationJournal: To Be Published
Title: SFX ferric 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 1.0Feb 12, 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: Deferrochelatase
B: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7004
Polymers88,4672
Non-polymers1,2332
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-63 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.567, 68.140, 74.800
Angle α, β, γ (deg.)90.00, 105.50, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 38.57 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7
Details: 1:1 v/v ratio of a solution containing 6.2 mg/ml Y389F DtpAa in 20 mM sodium phosphate, 150 mM NaCl pH 7 with a precipitant solution consisting of 100 mM HEPES pH 7 and 15% PEG 6000 to give ...Details: 1:1 v/v ratio of a solution containing 6.2 mg/ml Y389F DtpAa in 20 mM sodium phosphate, 150 mM NaCl pH 7 with a precipitant solution consisting of 100 mM HEPES pH 7 and 15% PEG 6000 to give a final volume of 400 ul.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.13 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: May 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 1.7→48.85 Å / Num. obs: 73582 / % possible obs: 100 % / Redundancy: 70.4 % / CC1/2: 0.879 / R split: 0.279 / Net I/σ(I): 3.13
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 5386 / CC1/2: 0.514 / R split: 0.753
Serial crystallography measurementCollection time total: 0.25 hours / Pulse duration: 10 fsec. / Pulse energy: 360 µJ / Pulse photon energy: 11 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetCrystals per unit: 25600 / Sample dehydration prevention: mylar / Sample holding: Silicon chip
Serial crystallography data reductionCrystal hits: 11101 / Frame hits: 11101 / Frames total: 49955

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→48.85 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.667 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20502 3803 4.9 %RANDOM
Rwork0.16695 ---
obs0.1688 73582 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.06 Å2
2---0.37 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.7→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5510 0 43 361 5914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0125746
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165073
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.6687847
X-RAY DIFFRACTIONr_angle_other_deg0.6491.5711751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.745732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.3831054
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6910792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026882
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021255
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_it2.241.8012919
X-RAY DIFFRACTIONr_mcbond_other2.2191.82918
X-RAY DIFFRACTIONr_mcangle_it2.9272.6963654
X-RAY DIFFRACTIONr_mcangle_other2.9292.6973655
X-RAY DIFFRACTIONr_scbond_it3.3392.0772827
X-RAY DIFFRACTIONr_scbond_other3.342.0772825
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7792.9914193
X-RAY DIFFRACTIONr_long_range_B_refined5.22523.0496279
X-RAY DIFFRACTIONr_long_range_B_other5.21722.9986256
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 297 -
Rwork0.257 5386 -
obs--100 %

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