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- PDB-6i8k: Dye type peroxidase Aa from Streptomyces lividans: 164 kGy structure -

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Basic information

Entry
Database: PDB / ID: 6i8k
TitleDye type peroxidase Aa from Streptomyces lividans: 164 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: 1.98 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
DepositionNov 20, 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
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-64 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.008, 68.281, 74.917
Angle α, β, γ (deg.)90.00, 105.79, 90.00
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.: 319 / 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: Jan 17, 2017
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.98→44.64 Å / Num. obs: 49513 / % possible obs: 100 % / Redundancy: 35.5 % / CC1/2: 0.969 / R split: 0.167 / Rmerge(I) obs: 0.705 / Net I/σ(I): 2.16
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 0.66 / CC1/2: 0.602 / R split: 0.627 / % 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
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
cctbx.primedata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I43

6i43


Resolution: 1.98→44.63 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.68
RfactorNum. reflection% reflection
Rfree0.2322 2008 4.06 %
Rwork0.1719 --
obs0.1744 49513 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 86 319 5947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075794
X-RAY DIFFRACTIONf_angle_d0.8817894
X-RAY DIFFRACTIONf_dihedral_angle_d7.9323992
X-RAY DIFFRACTIONf_chiral_restr0.047823
X-RAY DIFFRACTIONf_plane_restr0.0061049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.02950.29791370.24133388X-RAY DIFFRACTION100
2.0295-2.08440.34341460.25593371X-RAY DIFFRACTION100
2.0844-2.14570.31221360.24963353X-RAY DIFFRACTION100
2.1457-2.2150.32071450.24663379X-RAY DIFFRACTION100
2.215-2.29410.30751490.22893368X-RAY DIFFRACTION100
2.2941-2.3860.29521410.22393359X-RAY DIFFRACTION100
2.386-2.49460.28661430.2223409X-RAY DIFFRACTION100
2.4946-2.62610.28841430.21283391X-RAY DIFFRACTION100
2.6261-2.79060.26621430.19853377X-RAY DIFFRACTION100
2.7906-3.0060.24491430.18433375X-RAY DIFFRACTION100
3.006-3.30840.22871430.16793415X-RAY DIFFRACTION100
3.3084-3.78690.19891460.13123402X-RAY DIFFRACTION100
3.7869-4.77030.17041440.11953418X-RAY DIFFRACTION100
4.7703-44.64090.17321490.12833500X-RAY DIFFRACTION100

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