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- PDB-6q3e: Dye type peroxidase Aa from Streptomyces lividans: 274.4 kGy structure -

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Basic information

Entry
Database: PDB / ID: 6q3e
TitleDye type peroxidase Aa from Streptomyces lividans: 274.4 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 coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsEbrahim, A. / Moreno-Chicano, T. / Worrall, J.A.R. / Strange, R.W. / Axford, D. / Sherrell, D.A. / Appleby, M. / Owen, R.L.
CitationJournal: Iucrj / Year: 2019
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.H. / Sherrell, D.A. / Duyvesteyn, H.M.E. / Owada, S. / Tono, K. / Sugimoto, H. / Strange, R.W. / Worrall, J.A.R. / ...Authors: Ebrahim, A. / Moreno-Chicano, T. / Appleby, M.V. / Chaplin, A.K. / Beale, J.H. / Sherrell, D.A. / Duyvesteyn, H.M.E. / Owada, S. / Tono, K. / Sugimoto, H. / Strange, R.W. / Worrall, J.A.R. / Axford, D. / Owen, R.L. / Hough, M.A.
History
DepositionDec 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.2Jan 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

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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
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-63 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.068, 68.384, 75.097
Angle α, β, γ (deg.)90.000, 105.850, 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 coelicolor A3(2) (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.: 211 / 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, 2018
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.03→44.7 Å / Num. obs: 46140 / % possible obs: 100 % / Redundancy: 44.5 % / CC1/2: 0.969 / R split: 0.179 / Rmerge(I) obs: 0.765 / Net I/σ(I): 2.02
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 0.5 / CC1/2: 0.506 / R split: 0.783 / % possible all: 99.6
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
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I43

6i43


Resolution: 2.03→37.386 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.83
RfactorNum. reflection% reflection
Rfree0.2491 1990 4.31 %
Rwork0.1816 --
obs0.1846 46139 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.76 Å2 / Biso mean: 32.5936 Å2 / Biso min: 11.7 Å2
Refinement stepCycle: final / Resolution: 2.03→37.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 146 211 5899
Biso mean--26.59 35.39 -
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
2.03-2.08080.34691480.281331083256
2.0808-2.1370.35051300.265431253255
2.137-2.19990.33621470.262531413288
2.1999-2.27090.33371420.252831253267
2.2709-2.3520.33721330.236731643297
2.352-2.44620.28441440.228731323276
2.4462-2.55750.28611420.228531383280
2.5575-2.69230.31181450.221731403285
2.6923-2.86090.30081450.209531463291
2.8609-3.08170.30471430.203831623305
3.0817-3.39170.26951390.177131533292
3.3917-3.8820.21521460.142631793325
3.882-4.88920.17391400.127131883328
4.8892-37.39270.17891460.137232483394

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