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Yorodumi- PDB-1kag: Crystal Structure of the Escherichia coli Shikimate Kinase I (AroK) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kag | ||||||
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Title | Crystal Structure of the Escherichia coli Shikimate Kinase I (AroK) | ||||||
Components | Shikimate kinase I | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information shikimate kinase / shikimate kinase activity / shikimate metabolic process / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / response to antibiotic / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å | ||||||
Authors | Romanowski, M.J. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proteins / Year: 2002 Title: Crystal structure of the Escherichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam. Authors: Romanowski, M.J. / Burley, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kag.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kag.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kag_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 1kag_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 1kag_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1kag_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/1kag ftp://data.pdbj.org/pub/pdb/validation_reports/ka/1kag | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19565.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AROK / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A6D7, shikimate kinase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.43 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG 5000 MME, 0.2M ammonium sulfate, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.05→20 Å / Num. all: 19149 / Num. obs: 19149 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.031 | ||||||||||||||||||
Reflection shell | Resolution: 2.03→2.13 Å / Rmerge(I) obs: 0.049 / % possible all: 99.9 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 19142 / Rmerge(I) obs: 0.031 | ||||||||||||||||||
Reflection shell | *PLUS Rmerge(I) obs: 0.049 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.05→19.58 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 769059.91 / 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: 67.2088 Å2 / ksol: 0.405494 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→19.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 9.8 % / Rfactor all: 0.2216 / Rfactor obs: 0.217 / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.217 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.279 / Rfactor Rwork: 0.195 / Rfactor obs: 0.195 |