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Yorodumi- PDB-1jyl: Catalytic Mechanism of CTP:phosphocholine Cytidylyltransferase fr... -
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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) | ||||||
Components | CTP:phosphocholine CytidylyltransferaseCholine-phosphate cytidylyltransferase | ||||||
Keywords | TRANSFERASE / LicC / 3D Structure / CTP:phosphocholine cytidylyltransferase | ||||||
Function / homology | Function and homology information biosynthetic process / nucleotidyltransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kwak, B.-Y. / Yun, M. / Park, H.-w. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jyl.cif.gz | 206.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jyl.ent.gz | 164.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/1jyl ftp://data.pdbj.org/pub/pdb/validation_reports/jy/1jyl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Streptococcus pneumoniae (bacteria) / Gene: LicC / Production host: Escherichia coli (E. coli) / References: UniProt: Q97QE9, UniProt: A0A0H2UQB5*PLUS #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CDC / [ #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
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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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