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Yorodumi- PDB-2ilv: crystal structure of multifunctional sialyltransferase from Paste... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ilv | |||||||||
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Title | crystal structure of multifunctional sialyltransferase from Pasteurella multocida with CMP and alpha-lactose bound | |||||||||
Components | Alpha-2,3/2,6-sialyltransferase/sialidase | |||||||||
Keywords | TRANSFERASE / sialyltransferase / CMP / alpha-lactose / two Rossmann domains | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pasteurella multocida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | |||||||||
Authors | Fisher, A.J. / Ni, L. | |||||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Crystal Structures of Pasteurella multocida Sialyltransferase Complexes with Acceptor and Donor Analogues Reveal Substrate Binding Sites and Catalytic Mechanism. Authors: Ni, L. / Chokhawala, H.A. / Cao, H. / Henning, R. / Ng, L. / Huang, S. / Yu, H. / Chen, X. / Fisher, A.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ilv.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ilv.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ilv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/2ilv ftp://data.pdbj.org/pub/pdb/validation_reports/il/2ilv | HTTPS FTP |
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-Related structure data
Related structure data | 2ihjC 2ihkC 2ihzC 2ex1S 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: 46598.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pasteurella multocida (bacteria) / Strain: Pm70 / Gene: Pm0188 / Plasmid: pET23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15KI8, EC: 2.4.99.4 |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose |
#3: Chemical | ChemComp-C5P / |
#4: 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: 2.67 Å3/Da / Density % sol: 53.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30%, PEG MME 2000, 0.2 M NaBr, 0.4% Triton X-100 soaked in 20 mM alpha-lactose for one hour, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 23, 2006 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→63.63 Å / Num. obs: 25036 / % possible obs: 93.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 31.564 Å2 / Rsym value: 0.083 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 4378 / Rsym value: 0.381 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EX1 Resolution: 2.27→63.12 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.904 / SU B: 14.802 / SU ML: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.434 Å2
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Refinement step | Cycle: LAST / Resolution: 2.27→63.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.329 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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