[English] 日本語
Yorodumi- PDB-3id9: Crystal structure of a MutT/NUDIX family protein from Bacillus th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3id9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a MutT/NUDIX family protein from Bacillus thuringiensis | ||||||
Components | MutT/NUDIX family protein | ||||||
Keywords | HYDROLASE / MutT/NUDIX family / Protein Structure Initiative II(PSI II) / NYSGXRC / 11181f / Structural Genomics / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus thuringiensis str. Al Hakam (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å | ||||||
Authors | Palani, K. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a MutT/NUDIX family protein from Bacillus thuringiensis Authors: Palani, K. / Burley, S.K. / Swaminathan, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3id9.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3id9.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 3id9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3id9_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3id9_full_validation.pdf.gz | 452.9 KB | Display | |
Data in XML | 3id9_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3id9_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/3id9 ftp://data.pdbj.org/pub/pdb/validation_reports/id/3id9 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19869.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis str. Al Hakam (bacteria) Strain: Strain AI Hakam / Gene: BALH_3260 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C3H476*PLUS #2: Chemical | ChemComp-SO4 / | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.5M Ammonium sulfate, 25% Glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2009 / Details: MIRRORS |
Radiation | Monochromator: Si(III) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→36.39 Å / Num. all: 51688 / Num. obs: 51688 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 50.8 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5188 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.55→36.39 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 80358.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.6193 Å2 / ksol: 0.344356 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.2 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→36.39 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: NONE | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|