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- PDB-2yk7: Structure of Neisseria LOS-specific sialyltransferase (NST), in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yk7 | ||||||
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Title | Structure of Neisseria LOS-specific sialyltransferase (NST), in complex with CMP-3F-Neu5Ac. | ||||||
![]() | CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() N-acetyllactosaminide alpha-2,3-sialyltransferase / lipopolysaccharide biosynthetic process / glycosyltransferase activity / cell outer membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lin, L.Y.C. / Rakic, B. / Chiu, C.P.C. / Lameignere, E. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.5 KB | Display | ![]() |
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PDB format | ![]() | 62.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 857.6 KB | Display | ![]() |
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Full document | ![]() | 863.4 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yk4SC ![]() 2yk5C ![]() 2yk6C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37522.109 Da / Num. of mol.: 1 / Fragment: DELTA29NST, RESIDUES 49-370 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 126E / NRCC4010 / Variant: L1 IMMUNOTYPE / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CSF / |
#3: Chemical | ChemComp-1PE / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
Sequence details | E40D, R102W, G168I, T242, AND K273N ARE NATURAL VARIANTS IN THE STRAIN N. MENINGITIDIS SEROTYPE B ...E40D, R102W, G168I, T242, AND K273N ARE NATURAL VARIANTS IN THE STRAIN N. MENINGITID |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.52 % / 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: 180MM TRI-SODIUM CITRATE, 5 MM MNCL2, 20%(V/V) PEG 1500, PH 6.25 . |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / 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: 2.18→83.33 Å / Num. obs: 19377 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.18→2.22 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 2.64 / % possible all: 84.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YK4 Resolution: 2.18→83.33 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.671 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.23 / 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: 29.876 Å2
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Refinement step | Cycle: LAST / Resolution: 2.18→83.33 Å
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Refine LS restraints |
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