+Open data
-Basic information
Entry | Database: PDB / ID: 1bys | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF NUC COMPLEXED WITH TUNGSTATE | ||||||
Components | PROTEIN (ENDONUCLEASE) | ||||||
Keywords | ENDONUCLEASE / PHOSPHODIESTERASE | ||||||
Function / homology | Function and homology information phosphorus metabolic process / phospholipase D / phospholipid biosynthetic process / endonuclease activity Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Stuckey, J.A. / Dixon, J.E. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Crystal structure of a phospholipase D family member. Authors: Stuckey, J.A. / Dixon, J.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bys.cif.gz | 45 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bys.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/1bys ftp://data.pdbj.org/pub/pdb/validation_reports/by/1bys | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 17175.416 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cellular location: PERIPLASM / Gene: NUC / Plasmid: PT7-7 / Species (production host): Escherichia coli / Cellular location (production host): PERIPLASM / Gene (production host): NUC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q46707, UniProt: Q79SE0*PLUS |
---|---|
#2: Chemical | ChemComp-WO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 Details: 10 MG/ML PROTEIN + 2M NH4SO4, 100MM TRIS-HCL, PH 7.5 | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Zhao, Y., (1997) Protein Sci., 6, 2655. | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→17.8 Å / Num. obs: 17248 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 6.94 % / Rsym value: 0.69 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6 % / Mean I/σ(I) obs: 20 / Rsym value: 0.15 / % possible all: 99 |
Reflection | *PLUS Num. measured all: 119802 / Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.15 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.15 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2 Å / Rfactor Rfree: 0.297 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.272 / Rfactor obs: 0.272 |