[English] 日本語
Yorodumi- PDB-1x1q: Crystal structure of tryptophan synthase beta chain from Thermus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x1q | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of tryptophan synthase beta chain from Thermus thermophilus HB8 | ||||||
Components | tryptophan synthase beta chain | ||||||
Keywords | LYASE / structural genomics / Thermus thermophilus / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Asada, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of tryptophan synthase beta chain from Thermus thermophilus HB8 Authors: Asada, Y. / Kunishima, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1x1q.cif.gz | 155 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1x1q.ent.gz | 128.4 KB | Display | PDB format |
PDBx/mmJSON format | 1x1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x1q_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1x1q_full_validation.pdf.gz | 457.9 KB | Display | |
Data in XML | 1x1q_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 1x1q_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/1x1q ftp://data.pdbj.org/pub/pdb/validation_reports/x1/1x1q | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is dimer |
-Components
#1: Protein | Mass: 45866.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16609, tryptophan synthase #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.36 % |
---|---|
Crystal grow | Temperature: 291 K / Method: microbatch / pH: 8.5 Details: 0.2M Magnesium Chloride, 0.1M Tris-HCl, 15 % w/v PEG 4000, pH 8.5, MICROBATCH, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9792 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 27, 2004 / Details: mirrors |
Radiation | Monochromator: Bending Magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 26974 / Num. obs: 26974 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 39.559 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.111 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.27 / Num. unique all: 2631 / Rsym value: 0.515 / % possible all: 99.5 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.6 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.1 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.6 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.026
|