[English] 日本語
Yorodumi- PDB-2cz4: Crystal structure of a putative PII-like signaling protein (TTHA0... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cz4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a putative PII-like signaling protein (TTHA0516) from Thermus thermophilus HB8 | ||||||
Components | hypothetical protein TTHA0516Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved hypothetical protein / PII-like signaling protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / ACETATE ION / : / Uncharacterized protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.93 Å | ||||||
Authors | Arai, R. / Fusatomi, E. / Kukimoto-Niino, M. / Kawaguchi, S. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative PII-like signaling protein (TTHA0516) from Thermus thermophilus HB8 Authors: Arai, R. / Fusatomi, E. / Kukimoto-Niino, M. / Kawaguchi, S. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2cz4.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2cz4.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 2cz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/2cz4 ftp://data.pdbj.org/pub/pdb/validation_reports/cz/2cz4 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
2 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 13586.346 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0516 / Plasmid: pHCEH / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: GenBank: 55980485, UniProt: Q5SKX7*PLUS #2: Chemical | #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 0.1M Sodium acetate, 1.75M NaCl, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97889, 0.97939, 0.96000 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 11, 2004 / Details: two dimensional focusing mirror | ||||||||||||
Radiation | Monochromator: Si double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 1.93→50 Å / Num. obs: 30273 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.085 / Net I/σ(I): 18.9 | ||||||||||||
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 2412 / Rsym value: 0.334 / % possible all: 77.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.93→49.11 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 499237.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.201 Å2 / ksol: 0.378132 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→49.11 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.93→2.05 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|