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Open data
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Basic information
Entry | Database: PDB / ID: 6vv4 | ||||||
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Title | Scabin (V109G) 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 | ![]() | 75.5 KB | Display | ![]() |
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PDB format | ![]() | 54.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 250.8 KB | Display | ![]() |
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Full document | ![]() | 250.7 KB | Display | |
Data in XML | ![]() | 924 B | Display | |
Data in CIF | ![]() | 3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vpaC ![]() 6vuvC ![]() 6vvfC ![]() 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: 21815.090 Da / Num. of mol.: 1 / Mutation: V109G 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: 2.3 Å3/Da / Density % sol: 46.55 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop 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 6M / Detector: PIXEL / Date: Feb 16, 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: 1.7→37.403 Å / Num. obs: 21470 / % possible obs: 98.09 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03897 / Rpim(I) all: 0.02359 / Rrim(I) all: 0.04565 / Net I/σ(I): 19.12 |
Reflection shell | Resolution: 1.7→1.761 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.178 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 1917 / CC1/2: 0.437 / Rpim(I) all: 0.8116 / % possible all: 88.14 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5DAZ Resolution: 1.7→37.403 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.44 / 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: 95.82 Å2 / Biso mean: 36.3223 Å2 / Biso min: 16.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→37.403 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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