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Yorodumi- PDB-2yk6: Structure of Neisseria LOS-specific sialyltransferase (NST), in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yk6 | ||||||
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Title | Structure of Neisseria LOS-specific sialyltransferase (NST), in complex with CDP. | ||||||
Components | CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / LIPOOLIGOSACCHARIDE SIALYLTRANSFERASE | ||||||
Function / homology | Function and homology information N-acetyllactosaminide alpha-2,3-sialyltransferase / lipopolysaccharide biosynthetic process / glycosyltransferase activity / cell outer membrane Similarity search - Function | ||||||
Biological species | NEISSERIA MENINGITIDIS SEROGROUP B (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.83 Å | ||||||
Authors | Lin, L.Y.C. / Rakic, B. / Chiu, C.P.C. / Lameignere, E. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structure and Mechanism of the Lipooligosaccharide Sialyltransferase from Neisseria Meningitidis Authors: Lin, L.Y.C. / Rakic, B. / Chiu, C.P.C. / Lameignere, E. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yk6.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yk6.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 2yk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yk6_validation.pdf.gz | 840.2 KB | Display | wwPDB validaton report |
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Full document | 2yk6_full_validation.pdf.gz | 846.4 KB | Display | |
Data in XML | 2yk6_validation.xml.gz | 16 KB | Display | |
Data in CIF | 2yk6_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/2yk6 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/2yk6 | HTTPS FTP |
-Related structure data
Related structure data | 2yk4C 2yk5SC 2yk7C 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: 37565.203 Da / Num. of mol.: 1 / Fragment: DELTA29NST, RESIDUES 49-370 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEISSERIA MENINGITIDIS SEROGROUP B (bacteria) Strain: 126E / NRCC4010 / Variant: L1 IMMUNOTYPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P72097, EC: 2.4.99.- |
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#2: Chemical | ChemComp-CDP / |
#3: Chemical | ChemComp-1PE / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Sequence details | E40D, R102W, G168I, AND K273N ARE NATURAL VARIANTS IN THE STRAIN N. MENINGITID |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.45 % / Description: NONE |
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Crystal grow | Method: vapor diffusion / pH: 4.4 Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION METHODS USING DROPS OF PROTEIN MIXED WITH AN EQUAL VOLUME OF PRECIPITANT: 100 MM SODIUM ACETATE (PH 4.2 - 4.4) 1.7 M DI-AMMONIUM SULFATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: X-RAY MIRRORS OSMIC VARIMAXHR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→70.71 Å / Num. obs: 11162 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.83→2.88 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.7 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YK5 Resolution: 2.83→70.71 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.883 / SU B: 12.501 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R Free: 0.376 / 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: 27.571 Å2
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Refinement step | Cycle: LAST / Resolution: 2.83→70.71 Å
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Refine LS restraints |
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