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- PDB-6vuv: Scabin (S117A) toxin from Streptomyces scabies -

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Basic information

Entry
Database: PDB / ID: 6vuv
TitleScabin (S117A) toxin from Streptomyces scabies
ComponentsScabin
KeywordsTOXIN / Transferase
Function / homology: / : / Scabin-like / nucleotide binding / Putative secreted protein
Function and homology information
Biological speciesStreptomyces scabiei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLyons, B. / Lidster, T. / Merrill, A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Toxins / Year: 2021
Title: Mapping the DNA-Binding Motif of Scabin Toxin, a Guanine Modifying Enzyme from Streptomyces scabies .
Authors: Vatta, M. / Lyons, B. / Heney, K.A. / Lidster, T. / Merrill, A.R.
History
DepositionFeb 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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 6, 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)21,8411
Polymers21,8411
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8870 Å2
Unit cell
Length a, b, c (Å)88.450, 60.850, 37.950
Angle α, β, γ (deg.)90.000, 99.600, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-347-

HOH

21A-394-

HOH

31A-437-

HOH

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Components

#1: Protein Scabin


Mass: 21841.170 Da / Num. of mol.: 1 / Mutation: S117A
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 BL21(DE3) (bacteria) / References: UniProt: C9Z6T8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM potassium chloride, 50 mM sodium cacodylate trihydrate, pH 6.0, 16% PEG1000, 0.5 mM spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 13, 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: 1.55→43.61 Å / Num. obs: 28826 / % possible obs: 99.71 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04171 / Rpim(I) all: 0.02314 / Rrim(I) all: 0.04781 / Net I/σ(I): 17.72
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.9209 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 2860 / CC1/2: 0.692 / Rpim(I) all: 0.5157 / % possible all: 99.62

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5DAZ

5daz


Resolution: 1.55→43.606 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2101 1441 5.01 %
Rwork0.1786 27350 -
obs0.1801 28791 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.88 Å2 / Biso mean: 33.4009 Å2 / Biso min: 15.65 Å2
Refinement stepCycle: final / Resolution: 1.55→43.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 0 151 1435
Biso mean---38.84 -
Num. residues----165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.55-1.60540.32671430.31332714
1.6054-1.66970.31051450.26312744
1.6697-1.74570.24791440.23952725
1.7457-1.83770.24991420.20832694
1.8377-1.95280.18921430.18762717
1.9528-2.10360.22731440.17942753
2.1036-2.31530.21951440.18032723
2.3153-2.65030.21711440.17792740
2.6503-3.33890.2151440.17132740
3.3389-43.6060.18121480.15772800

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