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- PDB-1jyl: Catalytic Mechanism of CTP:phosphocholine Cytidylyltransferase fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jyl | ||||||
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Title | Catalytic Mechanism of CTP:phosphocholine Cytidylyltransferase from Streptococcus pneumoniae (LicC) | ||||||
![]() | CTP:phosphocholine Cytidylyltransferase | ||||||
![]() | TRANSFERASE / LicC / 3D Structure / CTP:phosphocholine cytidylyltransferase | ||||||
Function / homology | ![]() biosynthetic process / nucleotidyltransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kwak, B.-Y. / Yun, M. / Park, H.-w. | ||||||
![]() | ![]() Title: Structure and mechanism of CTP:phosphocholine cytidylyltransferase (LicC) from Streptococcus pneumoniae. Authors: Kwak, B.Y. / Zhang, Y.M. / Yun, M. / Heath, R.J. / Rock, C.O. / Jackowski, S. / Park, H.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206.5 KB | Display | ![]() |
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PDB format | ![]() | 164.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 629.7 KB | Display | ![]() |
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Full document | ![]() | 678.1 KB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 37.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29711.557 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CDC / [ #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.53 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium acetate, PEG 4000, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 291K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Jun 11, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 37757 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.24 Å2 / Rsym value: 0.094 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 1.82 % / Mean I/σ(I) obs: 2.02 / Num. unique all: 1522 / Rsym value: 0.33 / % possible all: 77.2 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 194300 / Rmerge(I) obs: 0.094 |
Reflection shell | *PLUS % possible obs: 77.2 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: XTALVIEW / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.208 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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