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- PDB-6i91: Dye type peroxidase Aa from Streptomyces lividans: 156.8 kGy structure -

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Basic information

Entry
Database: PDB / ID: 6i91
TitleDye type peroxidase Aa from Streptomyces lividans: 156.8 kGy structure
ComponentsDeferrochelatase/peroxidase
KeywordsOXIDOREDUCTASE / Dye type peroxidase / dose series / serial crystallography / heme
Function / homology
Function and homology information


ferrochelatase activity / iron import into cell / cell envelope / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsEbrahim, A. / Moreno-Chicano, T. / Worrall, J.A.R. / Strange, R.W. / Axford, D. / Sherrell, D.A. / Appleby, M. / Owen, R.L.
CitationJournal: To be published
Title: Dose-resolved serial synchrotron and XFEL structures of radiation sensitive metalloproteins
Authors: Ebrahim, A. / Moreno-Chicano, T. / Appleby, M.V. / Chaplin, A.K. / Beale, J. / Sherrell, D.A. / Duyvesteyn, H.M.E. / Owada, S. / Tono, K. / Sugimoto, S. / Strange, R.W. / Worrall, J.A.R. / ...Authors: Ebrahim, A. / Moreno-Chicano, T. / Appleby, M.V. / Chaplin, A.K. / Beale, J. / Sherrell, D.A. / Duyvesteyn, H.M.E. / Owada, S. / Tono, K. / Sugimoto, S. / Strange, R.W. / Worrall, J.A.R. / Axford, D. / Owen, R. / Hough, M.A.
History
DepositionNov 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: Deferrochelatase/peroxidase
B: Deferrochelatase/peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7774
Polymers78,5442
Non-polymers1,2332
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-64 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.042, 68.368, 74.974
Angle α, β, γ (deg.)90.000, 105.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deferrochelatase/peroxidase


Mass: 39272.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SCO2276 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9RKQ2, 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: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.16 % / Description: Microcrystals
Crystal growTemperature: 293 K / Method: batch mode / pH: 8
Details: 7 mg/ml protein mixed with 17% PEG 1500 and 67 mM MIB buffer (comprising imidazole, malonate and boric acid)

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2017
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.78→44.7 Å / Num. obs: 68910 / % possible obs: 100 % / Redundancy: 47.4 % / CC1/2: 0.956 / R split: 0.181 / Rmerge(I) obs: 0.884 / Net I/σ(I): 2.58
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 0.61 / CC1/2: 0.521 / R split: 0.714 / % possible all: 99.8
Serial crystallography measurementCollection time total: 0.25 hours / Collimation: 2x Kirkpatrick-Baez mirror pairs
Serial crystallography sample deliveryDescription: Silicon nitride chips / Method: fixed target

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
cctbx.primedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5map

5map


Resolution: 1.78→37.386 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.66
RfactorNum. reflection% reflection
Rfree0.2321 1993 2.92 %
Rwork0.1776 --
obs0.1792 68180 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.13 Å2 / Biso mean: 27.6917 Å2 / Biso min: 10.98 Å2
Refinement stepCycle: final / Resolution: 1.78→37.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 146 491 6179
Biso mean--22.25 34.8 -
Num. residues----723
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.78-1.82450.31871460.272246684814
1.8245-1.87380.32521340.275847314865
1.8738-1.9290.28741400.257746724812
1.929-1.99120.32351410.252647114852
1.9912-2.06240.31581420.24147144856
2.0624-2.1450.27681420.227447184860
2.145-2.24260.25921420.211446894831
2.2426-2.36080.26851420.203347464888
2.3608-2.50870.2741450.197747074852
2.5087-2.70230.23931430.194247324875
2.7023-2.97420.27081440.182447424886
2.9742-3.40430.24211440.164647464890
3.4043-4.28810.17031430.130747524895
4.2881-37.39380.17171450.131548595004

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