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Yorodumi- PDB-2ii6: Crystal structure of Pasteurella multocida sialyltransferase D141... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ii6 | ||||||
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Title | Crystal structure of Pasteurella multocida sialyltransferase D141N mutant in open conformation with CMP bound | ||||||
Components | Alpha-2,3/2,6-sialyltransferase/sialidase | ||||||
Keywords | TRANSFERASE / mutant D141N / sialyltransferase / streak seeding / CMP / two Rossmann domains | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pasteurella multocida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Fisher, A.J. / Ni, L. | ||||||
Citation | Journal: To be Published Title: Structural analysis of multifunctional sialyltransferase from Pasteurella multocida. Authors: Ni, L. / Huang, S. / Yu, H. / Sun, M. / Cao, 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 | 2ii6.cif.gz | 105.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ii6.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ii6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ii6_validation.pdf.gz | 784.2 KB | Display | wwPDB validaton report |
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Full document | 2ii6_full_validation.pdf.gz | 786.8 KB | Display | |
Data in XML | 2ii6_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 2ii6_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/2ii6 ftp://data.pdbj.org/pub/pdb/validation_reports/ii/2ii6 | HTTPS FTP |
-Related structure data
Related structure data | 2iibC 2iiqC 2ex0S 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: 46466.480 Da / Num. of mol.: 1 / Fragment: alpha2,3-silayltransferase / 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: 1.93 Å3/Da / Density % sol: 36.18 % |
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Crystal grow | pH: 7.5 Details: 25% PEG3350, 0.1 M NaCl, 0.1 M HEPES, 0.4% Triton X-100, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 6, 2006 / Details: DOUBLE CRYSTAL MONOCHROMATOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→31.02 Å / Num. all: 36710 / Num. obs: 35649 / % possible obs: 97.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 15.472 Å2 / Rsym value: 0.107 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 2678 / Rsym value: 0.191 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EX0 Resolution: 1.75→31.02 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.895 / SU B: 5.563 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.147 / 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: 19.673 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→31.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 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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