[English] 日本語
Yorodumi- PDB-2g1j: Crystal structure of Mycobacterium tuberculosis Shikimate Kinase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g1j | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis Shikimate Kinase at 2.0 angstrom resolution | ||||||
Components | Shikimate kinase | ||||||
Keywords | TRANSFERASE / shikimate pathway / shikimate kinase / ternary complex / drug design | ||||||
Function / homology | Function and homology information shikimate kinase / shikimate kinase activity / shikimate metabolic process / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Gan, J. / Gu, Y. / Li, Y. / Yan, H. / Ji, X. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Crystal Structure of Mycobacterium tuberculosis Shikimate Kinase in Complex with Shikimic Acid and an ATP Analogue. Authors: Gan, J. / Gu, Y. / Li, Y. / Yan, H. / Ji, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2g1j.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2g1j.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 2g1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/2g1j ftp://data.pdbj.org/pub/pdb/validation_reports/g1/2g1j | HTTPS FTP |
---|
-Related structure data
Related structure data | 1zyuC 2g1kC 1l4uS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18612.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: aroK / Plasmid: PET-17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0A4Z2, UniProt: P9WPY3*PLUS, shikimate kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.86 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 6.5 Details: 30% PEG5000, pH 6.5, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: BRUKER PROTEUM 300 / Detector: CCD / Date: Oct 14, 2004 / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 24308 / Num. obs: 24308 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2336 / % possible all: 91.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1L4U Resolution: 2→29.53 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 368890.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Details: Crystal is twined. Twin operator H, -H-K, -L. Twin fraction 0.50.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.7097 Å2 / ksol: 0.372625 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.53 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|