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Yorodumi- PDB-3baf: Crystal structure of shikimate kinase from Mycobacterium tubercul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3baf | ||||||
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Title | Crystal structure of shikimate kinase from Mycobacterium tuberculosis in complex with AMP-PNP | ||||||
Components | Shikimate kinase | ||||||
Keywords | TRANSFERASE / shikimate kinase / shikimate pathway / AMP-PNP / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / ATP-binding / Cytoplasm / Magnesium / Metal-binding / Nucleotide-binding | ||||||
Function / homology | Function and homology information shikimate kinase / shikimate metabolic process / shikimate kinase activity / 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: 2.25 Å | ||||||
Authors | Faim, L.M. / Dias, M.V.B. / Vasconcelos, I.G. / Basso, L.A. / Santos, D.S. / Azevedo, W.F. / Ruggiero, N.J. | ||||||
Citation | Journal: To be Published Title: Crystal Structure for shikimate kinase from Mycobacterium tuberculosis in complex with AMP-PNP Authors: Faim, L.M. / Dias, M.V.B. / Vasconcelos, I.G. / Basso, L.A. / Santos, D.S. / Azevedo, W.F. / Ruggiero, N.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3baf.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3baf.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 3baf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/3baf ftp://data.pdbj.org/pub/pdb/validation_reports/ba/3baf | HTTPS FTP |
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-Related structure data
Related structure data | 1zyuS 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: pET23a / Production host: Escherichia coli (E. coli) References: UniProt: P0A4Z2, UniProt: P9WPY3*PLUS, shikimate kinase |
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#2: Chemical | ChemComp-ANP / |
#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: 3.43 Å3/Da / Density % sol: 64.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 / Details: PEG, pH8, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 17, 2007 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.427 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→37.42 Å / Num. obs: 12600 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.19 / Rsym value: 0.13 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.19 / Num. unique all: 1816 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZYU Resolution: 2.25→37.42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.165 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.222 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.889 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→37.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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