[English] 日本語
![](img/lk-miru.gif)
- PDB-6ppx: Crystal structure of metal-free NeuB, an N-acetylneuraminate synt... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6ppx | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of metal-free NeuB, an N-acetylneuraminate synthase from Neisseria meningitidis in complex with malate | |||||||||
![]() | N-acetylneuraminate synthase | |||||||||
![]() | BIOSYNTHETIC PROTEIN / TRANSFERASE / NeuB / sialic acid synthase / N-acetylneuraminate synthase | |||||||||
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.S. / Berti, P.J. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 96.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 64.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 429.7 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ppwC ![]() 6ppyC ![]() 6ppzC ![]() 1xuzS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
|
-
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: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-MLT / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.95 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 3% (v/v) MPD 1.75M Malic acid 10mM magnesium chloride 10mM N-acetylneuraminic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 29, 2008 |
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: 1.85→77.62 Å / Num. obs: 29645 / % possible obs: 98.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 23.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.035 / Rrim(I) all: 0.104 / Net I/σ(I): 2.53 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2676 / CC1/2: 0.915 / Rpim(I) all: 0.248 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1XUZ Resolution: 1.85→46.48 Å / SU ML: 0.2857 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1387
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→46.48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|