[English] 日本語
Yorodumi- PDB-1geq: Entropic stabilization of the tryptophan synthase A-subunit from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1geq | ||||||
---|---|---|---|---|---|---|---|
Title | Entropic stabilization of the tryptophan synthase A-subunit from a hyperthermophile, pyrococcus furiosus: X-ray analysis and calorimetry | ||||||
Components | TRYPTOPHAN SYNTHASE ALPHA-SUBUNIT | ||||||
Keywords | LYASE / Tryptophan Synthase alpha-Subunit / Hyperthermophile / Pyrococcus furiosus / X-ray Analysis / Stability / Calorimetry | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å | ||||||
Authors | Yutani, K. / Yamagata, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry. Authors: Yamagata, Y. / Ogasahara, K. / Hioki, Y. / Lee, S.J. / Nakagawa, A. / Nakamura, H. / Ishida, M. / Kuramitsu, S. / Yutani, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1geq.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1geq.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 1geq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/1geq ftp://data.pdbj.org/pub/pdb/validation_reports/ge/1geq | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 27535.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PA1974 / Production host: Escherichia coli (E. coli) / Strain (production host): E.COLI-109 / References: UniProt: Q8U094, tryptophan synthase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.02 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES-NaOH, 12% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K | |||||||||||||||
Crystal | *PLUS Density % sol: 53.4 % | |||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Apr 23, 1999 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 31934 / Num. obs: 31934 / % possible obs: 94.2 % / Redundancy: 2.84 % / Rmerge(I) obs: 0.0353 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.67 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 7.3 / Num. unique all: 1557 / % possible all: 93.9 |
Reflection | *PLUS Num. measured all: 90544 / Rmerge(I) obs: 0.035 |
Reflection shell | *PLUS % possible obs: 93.9 % |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2→40 Å / Isotropic thermal model: Isotropic / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.02 Å
|