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- PDB-3n2e: Crystal structure of Helicobactor pylori shikimate kinase in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3n2e | ||||||
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Title | Crystal structure of Helicobactor pylori shikimate kinase in complex with NSC162535 | ||||||
![]() | Shikimate kinase | ||||||
![]() | TRANSFERASE / alpha-beta-alpha fold | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cheng, W.C. / Chen, T.J. / Lin, S.C. / Wang, W.C. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.2 KB | Display | ![]() |
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PDB format | ![]() | 82.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 986.5 KB | Display | ![]() |
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Full document | ![]() | 1005.2 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hr7C ![]() 3mrsC ![]() 3mufC ![]() 1zuhS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19004.135 Da / Num. of mol.: 3 / Mutation: E114A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-TLA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 0.1M sodium HEPES, 1.2M potassium sodium tartrate tetrahydrate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→30 Å / Num. all: 21908 / Num. obs: 21900 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 26.88 |
Reflection shell | Resolution: 2.53→2.62 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4.33 / Num. unique all: 2150 / Rsym value: 0.305 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZUH Resolution: 2.53→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.915 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.292 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.303 Å2
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Refinement step | Cycle: LAST / Resolution: 2.53→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.528→2.593 Å / Total num. of bins used: 20
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