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Yorodumi- PDB-2iib: Crystal structure of Pasteurella multocida sialyltransferase D141... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iib | ||||||
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Title | Crystal structure of Pasteurella multocida sialyltransferase D141N mutant with CMP bound | ||||||
Components | Alpha-2,3/2,6-sialyltransferase/sialidase | ||||||
Keywords | TRANSFERASE / mutant D141N / sialyltransferase / CMP / two Rossmann domains | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pasteurella multocida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 2iib.cif.gz | 99.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iib.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 2iib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iib_validation.pdf.gz | 845.3 KB | Display | wwPDB validaton report |
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Full document | 2iib_full_validation.pdf.gz | 848.1 KB | Display | |
Data in XML | 2iib_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 2iib_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/2iib ftp://data.pdbj.org/pub/pdb/validation_reports/ii/2iib | HTTPS FTP |
-Related structure data
Related structure data | 2ii6C 2iiqC 2ex1S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46466.480 Da / Num. of mol.: 1 / Mutation: D141N 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: Chemical | ChemComp-C5P / |
#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: 2.62 Å3/Da / Density % sol: 52.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 3,350, 0.1 M NaCl, 0.1 M HEPES, 0.4% Triton X-100, pH 7.5, 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 7, 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→64.1 Å / Num. all: 33560 / Num. obs: 33533 / % possible obs: 99.92 % / Redundancy: 4.65 % / Biso Wilson estimate: 20.07 Å2 / Rsym value: 0.0806 / Net I/σ(I): 6.09 |
Reflection shell | Resolution: 2→2.09 Å / Mean I/σ(I) obs: 1.29 / Num. unique all: 4212 / Rsym value: 0.3162 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EX1 Resolution: 2.2→63.5 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.879 / SU B: 8.288 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.204 / 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: 21.366 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→63.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 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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