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Yorodumi- PDB-2dfn: Structure of shikimate kinase from Mycobacterium tuberculosis com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dfn | ||||||
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Title | Structure of shikimate kinase from Mycobacterium tuberculosis complexed with ADP and shikimate at 1.9 angstrons of resolution | ||||||
Components | Shikimate kinase | ||||||
Keywords | TRANSFERASE / alpha/beta / shikimate pathway | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Dias, M.V. / Faim, L.M. / Vasconcelos, I.B. / de Oliveira, J.S. / Basso, L.A. / Santos, D.S. / de Azevedo, W.F. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2007 Title: Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis Authors: Dias, M.V. / Faim, L.M. / Vasconcelos, I.B. / de Oliveira, J.S. / Basso, L.A. / Santos, D.S. / de Azevedo, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dfn.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dfn.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 2dfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/2dfn ftp://data.pdbj.org/pub/pdb/validation_reports/df/2dfn | HTTPS FTP |
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-Related structure data
Related structure data | 2dftC 1we2S C: citing same article (ref.) 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 / Production host: Escherichia coli (E. coli) References: UniProt: P0A4Z2, UniProt: P9WPY3*PLUS, shikimate kinase |
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#2: Chemical | ChemComp-CL / |
#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: 2.84 Å3/Da / Density % sol: 56.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: 0.1M tris-HCl, 17% PEG 1500, 0.5-0.7M LiCl, pH 8.0, 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: RIGAKU / Detector: IMAGE PLATE / Date: Jun 7, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.427 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→35.16 Å / Num. all: 16169 / Num. obs: 16017 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 1.93→2.03 Å / Redundancy: 4.6 % / Num. unique all: 2160 / % possible all: 21.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WE2 Resolution: 1.93→35.16 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.963 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.159 / ESU R Free: 0.165 / 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: 32.718 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→35.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.98 Å / Total num. of bins used: 20
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