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Yorodumi- PDB-1zyu: Crystal structure of Mycobacterium tuberculosis shikimate kinase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zyu | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimate and amppcp at 2.85 angstrom resolution | ||||||
Components | Shikimate kinase | ||||||
Keywords | SIGANLING PROTEIN / 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: 2.9 Å | ||||||
Authors | Gan, J.H. / Gu, Y.J. / Li, Y. / Yan, H.G. / 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.H. / Gu, Y.J. / Li, Y. / Yan, H.G. / Ji, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zyu.cif.gz | 47.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zyu.ent.gz | 32.6 KB | Display | PDB format |
PDBx/mmJSON format | 1zyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/1zyu ftp://data.pdbj.org/pub/pdb/validation_reports/zy/1zyu | HTTPS FTP |
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-Related structure data
Related structure data | 2g1jC 2g1kC 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
#1: Protein | Mass: 18612.352 Da / Num. of mol.: 1 / Fragment: residues 1 -- 176 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 | ChemComp-ACP / |
#3: Chemical | ChemComp-SKM / ( |
#4: 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: 2.87 Å3/Da / Density % sol: 55.4 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG 3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, 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: Apr 19, 2005 / 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: 2.85→28.78 Å / Num. all: 4580 / Num. obs: 4580 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.85→3.03 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 1.7 / % possible all: 44.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L4U Resolution: 2.9→28.78 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 148980.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.9218 Å2 / ksol: 0.360743 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→28.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
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Xplor file |
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