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- PDB-6q34: Dye type peroxidase Aa from Streptomyces lividans: 196 kGy structure -

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Basic information

Entry
Database: PDB / ID: 6q34
TitleDye type peroxidase Aa from Streptomyces lividans: 196 kGy structure
ComponentsDeferrochelatase/peroxidase
KeywordsOXIDOREDUCTASE / Dye type peroxidase / dose series / serial crystallography / heme
Function / homology
Function and homology information


iron import into cell / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Deferrochelatase / 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/peroxidase
Similarity search - Component
Biological speciesStreptomyces lividans TK24 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 3, 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-63 kcal/mol
Surface area27320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.057, 68.370, 75.033
Angle α, β, γ (deg.)90.000, 105.810, 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 TK24 (bacteria) / Gene: SLIV_26340 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A076MF68, 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.: 438 / 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: 1.82→44.7 Å / Num. obs: 64459 / % possible obs: 100 % / Redundancy: 46 % / CC1/2: 0.966 / R split: 0.174 / Rmerge(I) obs: 0.851 / Net I/σ(I): 2.43
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 0.55 / CC1/2: 0.506 / R split: 0.75 / % possible all: 99.5
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 / Resolution: 1.82→37.383 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.29
RfactorNum. reflection% reflection
Rfree0.2359 2010 3.15 %
Rwork0.1798 --
obs0.1816 63829 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.82 Å2 / Biso mean: 29.0933 Å2 / Biso min: 10.87 Å2
Refinement stepCycle: final / Resolution: 1.82→37.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 146 438 6126
Biso mean--23.16 35.86 -
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
1.82-1.86550.32621410.262243524493
1.8655-1.9160.33781430.263443964539
1.916-1.97240.3151440.267743984542
1.9724-2.0360.3261450.253243974542
2.036-2.10880.32431380.247243594497
2.1088-2.19320.29151450.232344104555
2.1932-2.2930.31341450.22444194564
2.293-2.41390.25791370.202343964533
2.4139-2.56510.2821490.202544054554
2.5651-2.76310.2561430.198844274570
2.7631-3.0410.25511400.187744354575
3.041-3.48080.19911490.164744344583
3.4808-4.38430.1831410.130544504591
4.3843-37.39120.18331500.133145414691

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