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Yorodumi- PDB-3hr7: Crystal structure of the shikimate kinase-sulfate complex from He... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hr7 | ||||||
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Title | Crystal structure of the shikimate kinase-sulfate complex from Helicobacter pylori | ||||||
Components | Shikimate kinase | ||||||
Keywords | TRANSFERASE / three-layer alpha/beta fold / nucleoside monophosphate (NMP) kinase family / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / ATP-binding / Kinase / Magnesium / Metal-binding / Nucleotide-binding | ||||||
Function / homology | Function and homology information shikimate kinase / 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 | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Cheng, W.C. / Wang, W.C. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism Authors: Cheng, W.C. / Chen, Y.F. / Wang, H.J. / Hsu, K.C. / Lin, S.C. / Chen, T.J. / Yang, J.M. / Wang, W.C. #1: Journal: J.Bacteriol. / Year: 2005 Title: Structural basis for shikimate-binding specificity of Helicobacter pylori shikimate kinase Authors: Cheng, W.C. / Chang, Y.N. / Wang, W.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hr7.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hr7.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 3hr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/3hr7 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/3hr7 | HTTPS FTP |
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-Related structure data
Related structure data | 3mrsC 3mufC 3n2eC 1zuhS 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: 19265.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: aroK / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P56073, shikimate kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG 8000, 0.2M lithium sulphate, 0.1M sodium acetate buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→74.33 Å / Num. obs: 49284 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.068 |
Reflection shell | Highest resolution: 1.8 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZUH Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.117 / ESU R Free: 0.117 / 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: 29.453 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.804→1.851 Å / Total num. of bins used: 20
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