[English] 日本語
Yorodumi- PDB-3anp: Crystal structure of Thermus thermophilus FadR, a TetR familly tr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3anp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Thermus thermophilus FadR, a TetR familly transcriptional repressor, in complex with lauroyl-CoA. | ||||||
Components | Transcriptional repressor, TetR family | ||||||
Keywords | TRANSCRIPTION / All Alpha Protein / Transcriptional Repressor / DNA / Acyl-CoA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Agari, Y. / Agari, K. / Sakamoto, K. / Kuramitsu, S. / Shinkai, A. | ||||||
Citation | Journal: Microbiology / Year: 2011 Title: TetR-family transcriptional repressor Thermus thermophilus FadR controls fatty acid degradation. Authors: Agari, Y. / Agari, K. / Sakamoto, K. / Kuramitsu, S. / Shinkai, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3anp.cif.gz | 184.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3anp.ent.gz | 154.6 KB | Display | PDB format |
PDBx/mmJSON format | 3anp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/3anp ftp://data.pdbj.org/pub/pdb/validation_reports/an/3anp | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23711.828 Da / Num. of mol.: 4 / Fragment: UNP Residues 2-203 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: FadR / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SM42 #2: Chemical | #3: Chemical | ChemComp-DAO / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow |
|
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2009 Details: vertically bent two dimensional focusing mirror coated in Rhodium | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 6.6 % / Av σ(I) over netI: 33.4 / Number: 347357 / Rmerge(I) obs: 0.09 / Χ2: 1.41 / D res high: 2.25 Å / D res low: 50 Å / Num. obs: 53003 / % possible obs: 98.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→50 Å / Num. all: 81796 / Num. obs: 81796 / % possible obs: 99.1 % / Redundancy: 7.2 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.302 / Net I/σ(I): 11.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: SAD | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Phasing dm | FOM : 0.65 / FOM acentric: 0.65 / FOM centric: 0.68 / Reflection: 48664 / Reflection acentric: 44564 / Reflection centric: 4100 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.95→26.09 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8365 / Data cutoff high absF: 2615321 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.9792 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.4 Å2 / Biso mean: 25.0904 Å2 / Biso min: 8.02 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→26.09 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||
Xplor file |
|