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- PDB-8rgs: Serial synchrotron in plate room temperature structure of Dye Typ... -

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Basic information

Entry
Database: PDB / ID: 8rgs
TitleSerial synchrotron in plate room temperature structure of Dye Type Peroxidase Aa
ComponentsDeferrochelatase
KeywordsOXIDOREDUCTASE / serial synchrotron crystallography / heme peroxidase / metalloproteins
Function / homology
Function and homology information


iron import into cell / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / lyase activity / heme binding / metal ion binding
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsThompson, A.J. / Hough, M.A. / Williams, L.J. / Worrall, J.A.R. / Sanchez-Weatherby, J. / Mikolajek, H. / Sandy, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light SourceSTU0436 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Efficient in situ screening of and data collection from microcrystals in crystallization plates.
Authors: Thompson, A.J. / Sanchez-Weatherby, J. / Williams, L.J. / Mikolajek, H. / Sandy, J. / Worrall, J.A.R. / Hough, M.A.
History
DepositionDec 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)81,7134
Polymers80,4802
Non-polymers1,2332
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-63 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.474, 67.765, 74.733
Angle α, β, γ (deg.)90.000, 105.700, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Deferrochelatase


Mass: 40240.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: SLI_2602 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A7U9DT46
#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.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7
Details: 1:3 v/v ratio of 10 mg/ml protein in 20 mM sodium phosphate, 150 mM NaCl, pH 7.0 and a mother liquor solution (12% v/v PEG 3350, 100 mM HEPES pH 7.0)

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.775 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Oct 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.775 Å / Relative weight: 1
ReflectionResolution: 1.79→69.77 Å / Num. obs: 65821 / % possible obs: 99.75 % / Redundancy: 98.9 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.99 / R split: 0.121 / Net I/σ(I): 21.8
Reflection shellResolution: 1.79→1.854 Å / Num. unique obs: 6543 / CC1/2: 0.315 / R split: 0.978
Serial crystallography sample deliveryDescription: In Plate / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Mitegen in situ-1 plate

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→69.77 Å / SU ML: 0.2607 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2281 1946 2.96 %
Rwork0.1886 63711 -
obs0.1898 65657 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.16 Å2
Refinement stepCycle: LAST / Resolution: 1.79→69.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5503 0 86 416 6005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00875799
X-RAY DIFFRACTIONf_angle_d1.05317914
X-RAY DIFFRACTIONf_chiral_restr0.0609829
X-RAY DIFFRACTIONf_plane_restr0.01351056
X-RAY DIFFRACTIONf_dihedral_angle_d15.25632064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.38511370.33834563X-RAY DIFFRACTION99.62
1.83-1.880.35591360.28694509X-RAY DIFFRACTION99.87
1.88-1.940.29011280.25714554X-RAY DIFFRACTION99.96
1.94-20.27681220.21784549X-RAY DIFFRACTION99.98
2-2.070.28051510.2124524X-RAY DIFFRACTION99.91
2.07-2.160.3241440.26474494X-RAY DIFFRACTION99.34
2.16-2.260.29151230.21074555X-RAY DIFFRACTION99.51
2.26-2.370.24581370.17894530X-RAY DIFFRACTION99.98
2.37-2.520.25621520.18484541X-RAY DIFFRACTION100
2.52-2.720.21241480.17924552X-RAY DIFFRACTION100
2.72-2.990.20941320.17514569X-RAY DIFFRACTION100
2.99-3.420.16311500.16524571X-RAY DIFFRACTION100
3.42-4.310.17641520.14894570X-RAY DIFFRACTION99.68
4.31-69.770.21781340.17254630X-RAY DIFFRACTION98.72

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