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Open data
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Basic information
Entry | Database: PDB / ID: 1e6c | ||||||
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Title | K15M MUTANT OF SHIKIMATE KINASE FROM ERWINIA CHRYSANTHEMI | ||||||
![]() | SHIKIMATE KINASE | ||||||
![]() | TRANSFERASE / MUTANT SHIKIMATE KINASE / PHOSPHORYL TRANSFER / ADP / SHIKIMATE PATHWAY / P-LOOP PROTEIN | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Maclean, J. / Krell, T. / Coggins, J.R. / Lapthorn, A.J. | ||||||
![]() | ![]() Title: Biochemical and X-Ray Crystallographic Studies on Shikimate Kinase: The Important Structural Role of the P-Loop Lysine Authors: Krell, T. / Maclean, J. / Boam, D.J. / Cooper, A. / Resmini, M. / Brocklehurst, K. / Kelly, S.M. / Price, N.C. / Lapthorn, A.J. / Coggins, J.R. #1: Journal: J.Mol.Biol. / Year: 1998 Title: The Three-Dimensional Structure of Shikimate Kinase Authors: Krell, T. / Coggins, J.R. / Lapthorn, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87 KB | Display | ![]() |
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PDB format | ![]() | 65.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.5 KB | Display | ![]() |
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Full document | ![]() | 430.2 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1shkS S: Starting model for refinement |
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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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.50176, 0.00043, -0.86501), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18993.812 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 224 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MPD / ( #5: Chemical | ChemComp-MRD / ( | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | CHAIN A, B ENGINEERED MUTATION LYS15MET ENZYME REACTION: ATP + SHIKIMATE = ADP + SHIKIMATE 3- ...CHAIN A, B ENGINEERED |
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Sequence details | REFERENCE: THE SEQUENCE IS DESCRIBED IN MINTON N.P., WHITEHEAD P.J., ATKINSON T., GILBERT H.J. ...REFERENCE: THE SEQUENCE IS DESCRIBED IN MINTON N.P., WHITEHEAD P.J., ATKINSON T., GILBERT H.J. NUCLEIC ACIDS RES. 17:1769-1769(1989). |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.6 % | ||||||||||||||||||||
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Crystal grow | pH: 8 Details: 10% PEG8000, 100MM TRIS/HCL BUFFER PH 8.0, 2.5MM ADP, 2.5MM SHIKIMATE, 10MM MGCL2 | ||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 1998 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→21.4 Å / Num. obs: 27407 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 19.073 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.348 / % possible all: 69.1 |
Reflection | *PLUS Num. measured all: 164162 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / % possible obs: 69 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SHK Resolution: 1.8→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16471 / ESU R Free: 0.14659 Details: HYDROGEN ATOM CONTRIBUTION AND EXTERNAL BULK SOLVENT CORRECTION WERE APPLIED AS FPART . THE SPACE GROUP ASSIGNMENT WAS EXTREMELY CLOSE BETWEEN P21 AND C2221. IT WAS DECIDED TO PROCEED WITH ...Details: HYDROGEN ATOM CONTRIBUTION AND EXTERNAL BULK SOLVENT CORRECTION WERE APPLIED AS FPART . THE SPACE GROUP ASSIGNMENT WAS EXTREMELY CLOSE BETWEEN P21 AND C2221. IT WAS DECIDED TO PROCEED WITH P21 AND USE STRICT NCS RESTRAINTS BETWEEN MONOMERS.
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Displacement parameters | Biso mean: 23.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |