[English] 日本語
Yorodumi- PDB-1wna: Crystal structure of the hypothetical protein TT1805 from Thermus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wna | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the hypothetical protein TT1805 from Thermus thermophillus HB8 | ||||||
Components | the hypothetical protein (TT1805) | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Thermus thermophillus / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | TTHA1528-like / hypothetical protein tt1805 / Domain of unknown function DUF3197 / TTHA1528-like superfamily / Protein of unknown function (DUF3197) / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.58 Å | ||||||
Authors | Pioszak, A.A. / Kishishita, S. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the hypothetical protein TT1805 from Thermus thermophillus HB8 Authors: Pioszak, A.A. / Kishishita, S. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wna.cif.gz | 34.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wna.ent.gz | 27 KB | Display | PDB format |
PDBx/mmJSON format | 1wna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/1wna ftp://data.pdbj.org/pub/pdb/validation_reports/wn/1wna | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 14389.194 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SI52 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.24 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 13% PEG 8000, 20% glycerol, 40mM Potassium dihydrogen phosphate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Type: SPRING-8 BEAMLINE / Wavelength: 0.97912, 0.97944, 0.964 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: May 24, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 1.58→37.12 Å / Num. obs: 36267 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.61446 % / Biso Wilson estimate: 21.6 Å2 / Rsym value: 0.071 / Net I/σ(I): 17.5556 | ||||||||||||
Reflection shell | Resolution: 1.58→1.64 Å / Mean I/σ(I) obs: 4.52941 / Rsym value: 0.234 / % possible all: 85.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.58→37.12 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 812070.46 / 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: 48.0179 Å2 / ksol: 0.361438 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→37.12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.58→1.64 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|