+Open data
-Basic information
Entry | Database: PDB / ID: 1qs2 | ||||||
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Title | CRYSTAL STRUCTURE OF VIP2 WITH NAD | ||||||
Components | ADP-RIBOSYLTRANSFERASE | ||||||
Keywords | TOXIN / ALPHA-BETA PROTEIN / PROTEIN-NAD COMPLEX / BINARY TOXIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Han, S. / Craig, J.A. / Putnam, C.D. / Carozzi, N.B. / Tainer, J.A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Evolution and mechanism from structures of an ADP-ribosylating toxin and NAD complex. Authors: Han, S. / Craig, J.A. / Putnam, C.D. / Carozzi, N.B. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qs2.cif.gz | 96 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qs2.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qs2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qs2_validation.pdf.gz | 471.5 KB | Display | wwPDB validaton report |
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Full document | 1qs2_full_validation.pdf.gz | 481.9 KB | Display | |
Data in XML | 1qs2_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1qs2_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/1qs2 ftp://data.pdbj.org/pub/pdb/validation_reports/qs/1qs2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 45556.496 Da / Num. of mol.: 1 / Fragment: MATURE VIP2 / Mutation: WILD TYPE Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH NAD / Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Bacillus cereus (bacteria) References: UniProt: Q844J9*PLUS, NAD+ ADP-ribosyltransferase |
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#2: Chemical | ChemComp-NAD / |
#3: 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: 2.96 Å3/Da / Density % sol: 58.49 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG200, 2-METHYL 2,4-PENTANEDIOL, NAD, BIS-TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. all: 118889 / Num. obs: 15370 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.309 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 118889 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Resolution: 2.7→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 40.05 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.82 Å / Total num. of bins used: 8
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.7 Å / Rfactor Rfree: 0.384 / Rfactor Rwork: 0.324 |