[English] 日本語
Yorodumi- PDB-8i2k: Crystal structure of transcriptional regulator pvrA from Pseudomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i2k | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of transcriptional regulator pvrA from Pseudomonas aeruginosa. | ||||||
Components | Putative transcriptional regulator, TetR family | ||||||
Keywords | DNA BINDING PROTEIN / Transcriptional regulator | ||||||
Function / homology | Tetracyclin repressor-like, C-terminal domain (WHG) / Tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / DNA binding / Putative transcriptional regulator, TetR family Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.303 Å | ||||||
Authors | Pramanik, A. / Datta, S. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of transcriptional regulator pvrA from Pseudomonas aeruginosa. Authors: Pramanik, A. / Datta, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8i2k.cif.gz | 166.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8i2k.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 8i2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i2k_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8i2k_full_validation.pdf.gz | 447.2 KB | Display | |
Data in XML | 8i2k_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 8i2k_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/8i2k ftp://data.pdbj.org/pub/pdb/validation_reports/i2/8i2k | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25071.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: PA14_25800 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0H2ZBS8 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.75 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG 3000, 100mM Tris, 200mM Nacl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Oct 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→31.96 Å / Num. obs: 21122 / % possible obs: 99.2 % / Redundancy: 18.7 % / CC1/2: 0.999 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique obs: 2059 / CC1/2: 0.96 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIRAS / Resolution: 2.303→22.368 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.49 / Stereochemistry target values: MLHL
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.303→22.368 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|