[English] 日本語
Yorodumi- PDB-1ox5: TOWARDS UNDERSTANDING THE MECHANISM OF THE COMPLEX CYCLIZATION RE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ox5 | ||||||
---|---|---|---|---|---|---|---|
Title | TOWARDS UNDERSTANDING THE MECHANISM OF THE COMPLEX CYCLIZATION REACTION CATALYZED BY IMIDAZOLE GLYCEROPHOSPHATE SYNTHASE | ||||||
Components | Imidazole glycerol phosphate synthase hisHF | ||||||
Keywords | TRANSFERASE / LYASE / COMPLEX CYCLIZATION / IMIDAZOLE GLYCEROPHOSPHATE SYNTHASE | ||||||
Function / homology | Function and homology information imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / oxo-acid-lyase activity / glutaminase / L-histidine biosynthetic process / glutaminase activity / glutamine metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Chaudhuri, B.N. / Smith, J.L. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Towards Understanding the Mechanism of the Complex Cyclization Reaction Catalyzed by Imidazole Glycerophosphate Synthase:Crystal Structures of a Ternary Complex and the Free Enzyme Authors: Chaudhuri, B.N. / Lange, S.C. / Myers, R.S. / Davisson, V.J. / Smith, J.L. #1: Journal: Biochemistry / Year: 2003 Title: Substrate-Induced Changes in the Ammonia Channel for Imidazole Glycerol Phosphate Synthase Authors: Myers, R.S. / Jensen, J.R. / Deras, I.L. / Smith, J.L. / Davisson, V.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ox5.cif.gz | 220.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ox5.ent.gz | 174.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ox5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/1ox5 ftp://data.pdbj.org/pub/pdb/validation_reports/ox/1ox5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ox4C 1ox6C 1jvnS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
| ||||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.8365, 0.1593, -0.5243), Vector: |
-Components
#1: Protein | Mass: 61566.289 Da / Num. of mol.: 2 / Fragment: AMIDOTRANSFERASE AND CYCLASE DOMAINS / Mutation: Cys83 residue is covalently modified by acivicin Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HIS7 / Production host: Escherichia coli (E. coli) References: UniProt: P33734, Transferases; Glycosyltransferases; Pentosyltransferases, Lyases; Carbon-carbon lyases; Oxo-acid-lyases #2: Chemical | ChemComp-NI / | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.1 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ammonium sulfate, MES, PEG MME 3000, pH 6.5, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Chaudhuri, B.N., (2001) Structure, 9, 987. / PH range low: 7 / PH range high: 6.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 |
Detector | Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 45678 / % possible obs: 100 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.5 Å |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 100 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1JVN Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.37 |