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- PDB-6ppy: Crystal structure of NeuNAc oxime complexed with NeuB, an N-acety... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ppy | |||||||||
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Title | Crystal structure of NeuNAc oxime complexed with NeuB, an N-acetylneuraminate synthase from Neisseria meningitidis | |||||||||
![]() | N-acetylneuraminate synthase | |||||||||
![]() | BIOSYNTHETIC PROTEIN / TRANSFERASE / NeuB / sialic acid synthase / inhibitor complex / N-acetyl-neuraminate synthase / NeuNAc oxime | |||||||||
Function / homology | ![]() N-acetylneuraminate synthase / N-acetylneuraminate synthase activity / N-acylneuraminate-9-phosphate synthase activity / glycosylation / carbohydrate biosynthetic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Rosanally, A.Z. / Junop, M.J. / Berti, P.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: NeuNAc Oxime: A Slow-Binding and Effectively Irreversible Inhibitor of the Sialic Acid Synthase NeuB. Authors: Popovic, V. / Morrison, E. / Rosanally, A.Z. / Balachandran, N. / Senson, A.W. / Szabla, R. / Junop, M.S. / Berti, P.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 | ![]() | 194.9 KB | Display | ![]() |
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PDB format | ![]() | 127.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ppwC ![]() 6ppxC ![]() 6ppzC ![]() 1xuzS 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: 38395.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: synC / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-OVY / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 1.75 M malic acid, pH 6.2 10 mM MgCl2 10 mM NeuNAc 10 mM hydroxylamine hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 6, 2007 |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.51 Å / Num. obs: 23512 / % possible obs: 98.5 % / Redundancy: 3.95 % / Biso Wilson estimate: 23.08 Å2 / Rmerge(I) obs: 0.116 / Χ2: 0.98 / Net I/av σ(I): 7.8 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.97 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1587 / Χ2: 1.13 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XUZ Resolution: 2→46.17 Å / SU ML: 0.2586 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5809
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→46.17 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -21.1346954873 Å / Origin y: 4.41387238964 Å / Origin z: -16.916293827 Å
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Refinement TLS group | Selection details: all |