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Yorodumi- PDB-2iy7: crystal structure of the sialyltransferase PM0188 with CMP-3FNeuAc -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iy7 | ||||||
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Title | crystal structure of the sialyltransferase PM0188 with CMP-3FNeuAc | ||||||
Components | LPHA-2,3/2,6-SIALYLTRANSFERASE/SIALIDASE | ||||||
Keywords | TRANSFERASE / SIALYLTRANSFERASE / CMP-3FNEUAC / HYPOTHETICAL PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PASTEURELLA MULTOCIDA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Kim, D.U. / Cho, H.S. | ||||||
Citation | Journal: Bmb Rep / Year: 2008 Title: Structural analysis of sialyltransferase PM0188 from Pasteurella multocida complexed with donor analogue and acceptor sugar. Authors: Kim, D.U. / Yoo, J.H. / Lee, Y.J. / Kim, K.S. / Cho, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iy7.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iy7.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 2iy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/2iy7 ftp://data.pdbj.org/pub/pdb/validation_reports/iy/2iy7 | HTTPS FTP |
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-Related structure data
Related structure data | 2c83C 2c84SC 2iy8C C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 45534.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PASTEURELLA MULTOCIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(BE3) / References: UniProt: Q15KI8 |
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#2: Chemical | ChemComp-CSF / |
#3: 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: 2.31 Å3/Da / Density % sol: 46.35 % Description: 2C84 IS THE STRUCTURE OF PM0188 COMPLEX WITH CMP |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 1043461 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.88 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C84 Resolution: 1.85→15 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 35.0224 Å2 / ksol: 0.382698 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.85→15 Å
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Refine LS restraints |
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Xplor file |
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