[English] 日本語
Yorodumi- PDB-1k8z: CRYSTAL STRUCTURE OF THE TRYPTOPHAN SYNTHASE BETA-SER178PRO MUTAN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k8z | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE TRYPTOPHAN SYNTHASE BETA-SER178PRO MUTANT COMPLEXED WITH N-[1H-INDOL-3-YL-ACETYL]GLYCINE ACID | ||||||
Components | (TRYPTOPHAN SYNTHASE ...) x 2 | ||||||
Keywords | LYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN BIOSYNTHESIS / PYRIDOXAL PHOSPHATE | ||||||
Function / homology | Function and homology information tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Weyand, M. / Schlichting, I. / Marabotti, A. / Mozzarelli, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structure of the beta Ser178--> Pro mutant of tryptophan synthase. A "knock-out" allosteric enzyme. Authors: Weyand, M. / Schlichting, I. / Herde, P. / Marabotti, A. / Mozzarelli, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1k8z.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1k8z.ent.gz | 112.6 KB | Display | PDB format |
PDBx/mmJSON format | 1k8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k8z_validation.pdf.gz | 485 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1k8z_full_validation.pdf.gz | 702.4 KB | Display | |
Data in XML | 1k8z_validation.xml.gz | 55.7 KB | Display | |
Data in CIF | 1k8z_validation.cif.gz | 72.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/1k8z ftp://data.pdbj.org/pub/pdb/validation_reports/k8/1k8z | HTTPS FTP |
-Related structure data
Related structure data | 1k7xC 1k8yC 1qopS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-TRYPTOPHAN SYNTHASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 28698.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: TRPA/TRPB / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase |
---|---|
#2: Protein | Mass: 42797.723 Da / Num. of mol.: 1 / Mutation: S178P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: TRPA/TRPB / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase |
-Non-polymers , 4 types, 380 molecules
#3: Chemical | ChemComp-IAG / |
---|---|
#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-PLP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.8 / Details: pH 7.80 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 11, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→43.4 Å / Num. obs: 79408 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 2.597 % / Rsym value: 0.063 / Net I/σ(I): 9.29 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 2.354 % / Mean I/σ(I) obs: 2.11 / Rsym value: 0.334 / % possible all: 96.1 |
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 79508 / Num. measured all: 206209 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 96.1 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.11 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QOP Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.914 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / % reflection Rfree: 5 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|