[English] 日本語
Yorodumi- PDB-2dg7: Crystal structure of the putative transcriptional regulator SCO03... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dg7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the putative transcriptional regulator SCO0337 from Streptomyces coelicolor A3(2) | ||||||
Components | putative transcriptional regulatorTranscriptional regulation | ||||||
Keywords | GENE REGULATION / helix-turn-helix motif / TetR family | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Hayashi, T. / Tanaka, Y. / Sakai, N. / Yao, M. / Tamura, T. / Tanaka, I. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the putative transcriptional regulator SCO0337 from Streptomyces coelicolor A3(2) Authors: Hayashi, T. / Tanaka, Y. / Sakai, N. / Yao, M. / Tamura, T. / Tanaka, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2dg7.cif.gz | 44 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2dg7.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/2dg7 ftp://data.pdbj.org/pub/pdb/validation_reports/dg/2dg7 | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -x+1, -y+1, z. |
-Components
#1: Protein | Mass: 21442.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Plasmid: pTip-QC2 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): L-88 / References: GenBank: 5912516, UniProt: Q9RK42*PLUS |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.57 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM HEPES pH7.0, 9% Jeffamine ED-2001 reagent pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97934, 0.97950, 0.98338 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2005 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 9138 / % possible obs: 99.7 % / Redundancy: 10.2 % / Biso Wilson estimate: 24.1 Å2 / Rsym value: 0.049 | ||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 9.4 % / Num. unique all: 872 / Rsym value: 0.204 / % possible all: 97.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.3→9.98 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1105378.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.8184 Å2 / ksol: 0.553281 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→9.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|