[English] 日本語
Yorodumi- PDB-1lbf: CRYSTAL STRUCTURE OF INDOLE-3-GLYCEROL PHOSPHATE SYNTASE (IGPS)WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lbf | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF INDOLE-3-GLYCEROL PHOSPHATE SYNTASE (IGPS)WITH REDUCED 1-(O-CABOXYPHENYLAMINO)-1-DEOXYRIBULOSE 5-PHOSPHATE (RCDRP) | ||||||
Components | INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE | ||||||
Keywords | LYASE / protein ligand complex / beta barrel / tryptophan biosynthesis / substrate analogue complex | ||||||
Function / homology | Function and homology information indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.05 Å | ||||||
Authors | Hennig, M. / Darimont, B. / Kirschner, K. / Jansonius, J.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: The catalytic mechanism of indole-3-glycerol phosphate synthase: crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product. Authors: Hennig, M. / Darimont, B.D. / Jansonius, J.N. / Kirschner, K. #1: Journal: Structure / Year: 1995 Title: 2.0 A structure of indole-3-glycerol phosphate synthase from the hyperthermophile Sulfolobus solfataricus: possible determinants of protein stability. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lbf.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lbf.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/1lbf ftp://data.pdbj.org/pub/pdb/validation_reports/lb/1lbf | HTTPS FTP |
---|
-Related structure data
Related structure data | 1a53C 1lblC 1igsS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28494.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) References: UniProt: Q06121, indole-3-glycerol-phosphate synthase |
---|---|
#2: Chemical | ChemComp-137 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 30% ammonium sulphate, 50 mM phosphate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 10, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→12 Å / Num. all: 114105 / Num. obs: 27283 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2.05→2.2 Å / % possible all: 95 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1IGS Resolution: 2.05→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→15 Å
| ||||||||||||||||||||
Refine LS restraints | Type: o_bond_d / Dev ideal: 0.013 |