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Open data
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Basic information
Entry | Database: PDB / ID: 6vvf | ||||||
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Title | Scabin (Y129H) toxin from Streptomyces scabies | ||||||
![]() | Scabin | ||||||
![]() | TOXIN / Transferase | ||||||
Function / homology | : / nucleotide binding / Putative secreted protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Heney, K. / Lyons, B. / Merrill, A.R. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.9 KB | Display | ![]() |
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PDB format | ![]() | 55.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 250.3 KB | Display | ![]() |
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Full document | ![]() | 250.3 KB | Display | |
Data in XML | ![]() | 1.1 KB | Display | |
Data in CIF | ![]() | 3.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vpaC ![]() 6vuvC ![]() 6vv4C ![]() 5dazS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Strain: 87.22 / Gene: SCAB_27771 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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