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Yorodumi- PDB-1u8a: Crystal Structure of Mycobacterium Tuberculosis Shikimate Kinase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u8a | ||||||
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Title | Crystal Structure of Mycobacterium Tuberculosis Shikimate Kinase in Complex with Shikimate and ADP at 2.15 Angstrom Resolution | ||||||
Components | Shikimate kinase | ||||||
Keywords | TRANSFERASE / SHIKIMATE PATHWAY / SHIKIMATE KINASE / 2 PHORSPHORYL TRANSFER / DRUG DESIGN | ||||||
Function / homology | Function and homology information shikimate kinase / shikimate metabolic process / Chorismate via Shikimate Pathway / shikimate kinase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Dhaliwal, B. / Nichols, C.E. / Ren, J. / Lockyer, M. / Charles, I. / Hawkins, A.R. / Stammers, D.K. | ||||||
Citation | Journal: Febs Lett. / Year: 2004 Title: Crystallographic studies of shikimate binding and induced conformational changes in Mycobacterium tuberculosis shikimate kinase. Authors: Dhaliwal, B. / Nichols, C.E. / Ren, J. / Lockyer, M. / Charles, I. / Hawkins, A.R. / Stammers, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u8a.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u8a.ent.gz | 33.2 KB | Display | PDB format |
PDBx/mmJSON format | 1u8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/1u8a ftp://data.pdbj.org/pub/pdb/validation_reports/u8/1u8a | HTTPS FTP |
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-Related structure data
Related structure data | 1l4yS S: Starting model for refinement |
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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
#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: pET17b / 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 | ChemComp-ADP / | #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: 2.79 Å3/Da / Density % sol: 55.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 2000, Lithium chloride, Tris-HCl, Adenosine-5'-diphospate, Shikimic acid, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 25, 2003 / Details: mirrors |
Radiation | Monochromator: Osmic Confocal Blue Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. all: 12161 / Num. obs: 12135 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 5.93 % / Biso Wilson estimate: 40.52 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 5.86 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 3.5 / Num. unique all: 606 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1L4Y Resolution: 2.15→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→30 Å
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Refine LS restraints |
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