+Open data
-Basic information
Entry | Database: PDB / ID: 6vvf | ||||||
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Title | Scabin (Y129H) toxin from Streptomyces scabies | ||||||
Components | Scabin | ||||||
Keywords | TOXIN / Transferase | ||||||
Function / homology | : / Putative secreted protein Function and homology information | ||||||
Biological species | Streptomyces scabiei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Heney, K. / Lyons, B. / Merrill, A.R. | ||||||
Funding support | Canada, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vvf.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vvf.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 6vvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/6vvf ftp://data.pdbj.org/pub/pdb/validation_reports/vv/6vvf | HTTPS FTP |
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-Related structure data
Related structure data | 6vpaC 6vuvC 6vv4C 5dazS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.17 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 15, 2019 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.72 Å2 / Biso mean: 33.7433 Å2 / Biso min: 12.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→28.62 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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