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Yorodumi- PDB-2iiq: Crystal structure of Pasteurella multocida sialyltransferase in a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iiq | ||||||
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Title | Crystal structure of Pasteurella multocida sialyltransferase in an open conformation with CMP bound | ||||||
Components | Alpha-2,3/2,6-sialyltransferase/sialidase | ||||||
Keywords | TRANSFERASE / sialyltransferase / CMP / streak seeding / two Rossmann domains | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pasteurella multocida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ni, L. / Fisher, A.J. | ||||||
Citation | Journal: To be Published Title: Structural analysis of multifunctional sialyltransferase from Pasteurella multocida. Authors: Ni, L. / Huang, S. / Yu, H. / Cao, H. / Sun, M. / 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 | 2iiq.cif.gz | 179 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iiq.ent.gz | 139.3 KB | Display | PDB format |
PDBx/mmJSON format | 2iiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/2iiq ftp://data.pdbj.org/pub/pdb/validation_reports/ii/2iiq | HTTPS FTP |
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-Related structure data
Related structure data | 2ii6C 2iibC 2ex0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 46467.465 Da / Num. of mol.: 2 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 #2: Chemical | #3: 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: 2.07 Å3/Da / Density % sol: 40.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25%, PEG 3350, 0.1 M NaCl, 0.1 M HEPES, 0.4% Triton X-100 streak seeded by apo crystals, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Jun 29, 2006 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→59.55 Å / Num. all: 39043 / Num. obs: 38951 / % possible obs: 99.76 % / Redundancy: 6.16 % / Biso Wilson estimate: 20.54 Å2 / Rsym value: 0.1001 / Net I/σ(I): 5.35 |
Reflection shell | Resolution: 2.2→2.3 Å / Mean I/σ(I) obs: 1.78 / Num. unique all: 4884 / Rsym value: 0.2421 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EX0 Resolution: 2.3→59.55 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 13.054 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.6 / ESU R Free: 0.277 / 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: 5.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→59.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 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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