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- PDB-6apy: Scabin (W128Y) toxin from Streptomyces scabies -

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Basic information

Entry
Database: PDB / ID: 6apy
TitleScabin (W128Y) toxin from Streptomyces scabies
ComponentsScabin
KeywordsTOXIN / transferase / bacterial toxin
Function / homology: / : / Scabin-like / nucleotide binding / Putative secreted protein
Function and homology information
Biological speciesStreptomyces scabiei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLyons, B. / Lidster, T. / Merrill, A.R.
CitationJournal: Biochem. J. / Year: 2018
Title: Characterization of the catalytic signature of Scabin toxin, a DNA-targeting ADP-ribosyltransferase.
Authors: Lyons, B. / Lugo, M.R. / Carlin, S. / Lidster, T. / Merrill, A.R.
History
DepositionAug 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 4, 2023Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Scabin


Theoretical massNumber of molelcules
Total (without water)21,8341
Polymers21,8341
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, Monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8480 Å2
Unit cell
Length a, b, c (Å)88.420, 60.750, 37.870
Angle α, β, γ (deg.)90.000, 99.610, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-387-

HOH

21A-421-

HOH

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Components

#1: Protein Scabin


Mass: 21834.135 Da / Num. of mol.: 1 / Mutation: W128Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces scabiei (strain 87.22) (bacteria)
Strain: 87.22 / Gene: SCAB_27771 / Production host: Escherichia coli (E. coli) / References: UniProt: C9Z6T8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 14% PEG400, 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 12, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→37.34 Å / Num. obs: 31670 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.024 / Rsym value: 0.049 / Net I/σ(I): 17.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRsym value% possible all
1.5-1.554.10.6622.231520.7670.3730.76299.9
1.55-1.624.10.4673.131470.870.2630.53799.8
1.62-1.694.20.3334.331430.9250.1870.38399.8
1.69-1.784.20.2375.931510.9650.1330.272100
1.78-1.894.20.1439.631760.9870.080.165100
1.89-2.044.20.08415.631450.9950.0470.09699.8
2.04-2.234.20.05821.531860.9970.0330.06799.9
2.24-2.564.20.04421.531600.9970.0250.051100
2.56-3.234.20.03138.731840.9990.0170.03599.9
3.23-37.344.20.03148.332260.9990.0170.03599.7

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5DAZ

5daz


Resolution: 1.5→37.34 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1792 1583 5 %
Rwork0.1504 --
obs-31670 99.8 %
Displacement parametersBiso mean: 24.86 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 0 130 1394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081359
X-RAY DIFFRACTIONf_angle_d0.9121883
X-RAY DIFFRACTIONf_chiral_restr0.057202
X-RAY DIFFRACTIONf_dihedral_angle_d13.733814
X-RAY DIFFRACTIONf_plane_restr0.006254
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection Rfree: 5 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.550.32021570.2288299199.8
1.55-1.620.22431570.1853298899.7
1.62-1.690.19611570.1541298499.8
1.69-1.780.19471580.1424299099.9
1.78-1.890.17221590.1258301599.9
1.89-2.040.16111560.1217298799.8
2.04-2.240.16341590.1319302799.9
2.24-2.560.16771580.14163002100
2.56-3.230.17321590.1539302599.9
3.23-37.340.17671620.1545306399.7

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