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- PDB-5uvq: Scabin (W155A) toxin from Streptomyces scabies -

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Basic information

Entry
Database: PDB / ID: 5uvq
TitleScabin (W155A) toxin from Streptomyces scabies
ComponentsScabin
KeywordsTRANSFERASE / 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: 1.6 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
DepositionFeb 20, 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Scabin


Theoretical massNumber of molelcules
Total (without water)21,7421
Polymers21,7421
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.110, 60.800, 38.370
Angle α, β, γ (deg.)90.000, 99.360, 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-335-

HOH

21A-373-

HOH

31A-423-

HOH

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Components

#1: Protein Scabin


Mass: 21742.039 Da / Num. of mol.: 1 / Fragment: UNP residues 29-200 / Mutation: W155A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces scabiei (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.: 129 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 15% PEG400, 0.1 M MES

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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 8, 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: 1.6→37.86 Å / Num. obs: 26414 / % possible obs: 100 % / Redundancy: 4.5 % / Biso Wilson estimate: 25.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rsym value: 0.06 / Net I/σ(I): 16.21
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.65 / Num. unique all: 2615 / Num. unique obs: 2615 / CC1/2: 0.82 / Rsym value: 0.95 / % possible all: 100

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Processing

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

5daz


Resolution: 1.6→37.86 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.186 1321 5 %
Rwork0.145 --
obs-26414 100 %
Displacement parametersBiso mean: 35.81 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 0 129 1383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_plane_restr0.007428
X-RAY DIFFRACTIONf_chiral_restr0.081201
X-RAY DIFFRACTIONf_dihedral_angle_d13.3241052
X-RAY DIFFRACTIONf_angle_d0.9584607
X-RAY DIFFRACTIONf_bond_d0.0112553
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.66410.28891460.2432277399.5
1.6641-1.73980.27491460.2136275599.6
1.7398-1.83160.22481450.1649275299.4
1.8316-1.94630.18291460.1286275999.7
1.9463-2.09660.17231450.1205276499.7
2.0966-2.30760.18911460.1277279499.7
2.3076-2.64140.18791470.1321278699.9
2.6414-3.32780.1751480.1515280699.9
3.3278-37.860.17651500.14382851100

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