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Yorodumi- PDB-2g1k: Crystal structure of Mycobacterium tuberculosis shikimate kinase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g1k | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimate at 1.75 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: 1.75 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g1k.cif.gz | 49.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g1k.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 2g1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/2g1k ftp://data.pdbj.org/pub/pdb/validation_reports/g1/2g1k | HTTPS FTP |
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-Related structure data
Related structure data | 1zyuC 2g1jC 1l4uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18612.352 Da / Num. of mol.: 1 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 | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SKM / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 4.5 Details: 2.0 M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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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 | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. all: 20830 / Num. obs: 20830 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1923 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1L4U Resolution: 1.75→28.49 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1123302.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.1977 Å2 / ksol: 0.370194 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→28.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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