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- PDB-6vvf: Scabin (Y129H) toxin from Streptomyces scabies -

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Basic information

Entry
Database: PDB / ID: 6vvf
TitleScabin (Y129H) 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: 1.75 Å
AuthorsHeney, K. / Lyons, B. / 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 17, 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)21,8321
Polymers21,8321
Non-polymers00
Water1,910106
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 area8700 Å2
Unit cell
Length a, b, c (Å)88.550, 60.230, 37.920
Angle α, β, γ (deg.)90.000, 99.380, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-358-

HOH

21A-375-

HOH

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Components

#1: Protein Scabin


Mass: 21832.143 Da / Num. of mol.: 1 / Fragment: UNP residues 29-200 / Mutation: Y129H
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.: 106 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 15, 2019
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: 1.75→28.62 Å / Num. obs: 19873 / % possible obs: 99.65 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04077 / Rpim(I) all: 0.02459 / Rrim(I) all: 0.04771 / Net I/σ(I): 18.48
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 2.14 % / Rmerge(I) obs: 0.7059 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 1976 / CC1/2: 0.821 / Rpim(I) all: 0.4305 / Rrim(I) all: 0.8289 / % possible all: 99.14

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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: 1.75→28.62 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2064 994 5.01 %
Rwork0.1708 18864 -
obs0.1725 19858 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.72 Å2 / Biso mean: 33.7433 Å2 / Biso min: 12.32 Å2
Refinement stepCycle: final / Resolution: 1.75→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 0 106 1387
Biso mean---38.64 -
Num. residues----164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7501-1.84240.31211410.2891267699
1.8424-1.95780.25391400.20822647100
1.9578-2.10890.22271430.17062723100
2.1089-2.3210.21571400.16832667100
2.321-2.65670.20791420.16112697100
2.6567-3.34630.19831430.16462707100
3.3463-28.620.18711450.1622747100

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