[English] 日本語
Yorodumi- PDB-3gpv: Crystal structure of a transcriptional regulator, MerR family fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gpv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a transcriptional regulator, MerR family from Bacillus thuringiensis | ||||||
Components | Transcriptional regulator, MerR family | ||||||
Keywords | transcription regulator / transcriptional regulator / MerR family / Protein Structure Initiative II(PSI II) / NYSGXRC / 11183m / Structural Genomics / New York SGX Research Center for Structural Genomics / DNA-binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus thuringiensis serovar konkukian (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Palani, K. / Kumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a transcriptional regulator, MerR family from Bacillus thuringiensis Authors: Palani, K. / Kumaran, D. / Burley, S.K. / Swaminathan, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gpv.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gpv.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 3gpv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/3gpv ftp://data.pdbj.org/pub/pdb/validation_reports/gp/3gpv | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | DIMER |
-Components
#1: Protein | Mass: 17897.451 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis serovar konkukian (bacteria) Gene: BT9727_1615 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6HKH9 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.14 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Magnesium chloride hexahydrate 0.1M Tris hydrochloride 30% Polyethylene glycol 4000, pH 8.5, 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: Feb 18, 2009 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE 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: 1.9→37.26 Å / Num. all: 21114 / Num. obs: 21114 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2 / Num. unique all: 942 / % possible all: 49.1 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.9→37.26 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 204997.19 / 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: 63.6475 Å2 / ksol: 0.381566 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.5 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→37.26 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|