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Yorodumi- PDB-1l4y: CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCUL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l4y | ||||||
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Title | CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MGADP AT 2.0 ANGSTROM RESOLUTION | ||||||
Components | SHIKIMATE KINASE | ||||||
Keywords | TRANSFERASE / SHIKIMATE PATHWAY / SHIKIMATE KINASE / PHORSPHORYL TRANSFER / DRUG DESIGN | ||||||
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 / Difference Fourier / Resolution: 2 Å | ||||||
Authors | Gu, Y. / Reshetnikova, L. / Li, Y. / Wu, Y. / Yan, H. / Singh, S. / Ji, X. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis. Authors: Gu, Y. / Reshetnikova, L. / Li, Y. / Wu, Y. / Yan, H. / Singh, S. / Ji, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l4y.cif.gz | 50.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l4y.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 1l4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l4y_validation.pdf.gz | 823.3 KB | Display | wwPDB validaton report |
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Full document | 1l4y_full_validation.pdf.gz | 826.2 KB | Display | |
Data in XML | 1l4y_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1l4y_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/1l4y ftp://data.pdbj.org/pub/pdb/validation_reports/l4/1l4y | HTTPS FTP |
-Related structure data
Related structure data | 1l4uSC 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 on special symmetry positions |
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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: 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-MG / | ||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-ADP / | #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: 2.91 Å3/Da / Density % sol: 57.74 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288.2 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, Magnesium Choloride, Sodium Chloride, ADENOSINE-5'-DIPHOSPHATE, SHIKIMIC ACID, Na-HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.2K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Gu, Y., (2001) Acta Crystallogr, D57, 1870. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 1999 / Details: MIRROR |
Radiation | Monochromator: Silicon (111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2→27.65 Å / Num. all: 15110 / Num. obs: 14820 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.88 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.056 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 4.64 / Num. unique all: 1461 / Rsym value: 0.41 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / % possible obs: 99.5 % / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.63 |
-Processing
Software |
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Refinement | Method to determine structure: Difference Fourier Starting model: PDB ENTRY 1L4U Resolution: 2→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 251349.94 / Data cutoff high rms absF: 251349.94 / 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: 50.129 Å2 / ksol: 0.376723 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.03 Å / Lowest resolution: 30 Å / Rfactor obs: 0.217 / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.217 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.298 / Rfactor Rwork: 0.274 / Rfactor obs: 0.274 |