[English] 日本語
Yorodumi- PDB-1w1x: Structure of Neuraminidase from English duck subtype N6 complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w1x | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Neuraminidase from English duck subtype N6 complexed with 30 mM sialic acid (NANA, Neu5Ac), crystal soaked for 3 hours at 277 K. | |||||||||
Components | NEURAMINIDASE | |||||||||
Keywords | HYDROLASE / INFLUENZA TYPE A / NEURAMINIDASE / HB SITE / SIALIC ACID / SUBTYPE N6 | |||||||||
Function / homology | Function and homology information exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | INFLUENZA A VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Rudino-Pinera, E. / Tunnah, P. / Crennell, S.J. / Webster, R.G. / Laver, W.G. / Garman, E.F. | |||||||||
Citation | Journal: To be Published Title: The Crystal Structure of Type a Influenza Virus Neuraminidase of the N6 Subtype Reveals the Existence of Two Separate Neu5Ac Binding Sites Authors: Rudino-Pinera, E. / Tunnah, P. / Crennell, S.J. / Webster, R.G. / Laver, W.G. / Garman, E.F. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1w1x.cif.gz | 362.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1w1x.ent.gz | 288.8 KB | Display | PDB format |
PDBx/mmJSON format | 1w1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/1w1x ftp://data.pdbj.org/pub/pdb/validation_reports/w1/1w1x | HTTPS FTP |
---|
-Related structure data
Related structure data | 1w20C 1w21C 2cmlC 1v0zS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 43011.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH SIALIC ACID / Source: (gene. exp.) INFLUENZA A VIRUS Description: INFLUENZA VIRUS GROWN IN EMBRIONATED CHICKEN EGGS Production host: GALLUS GALLUS (chicken) / References: UniProt: Q6XV27, exo-alpha-sialidase |
---|
-Sugars , 9 types, 25 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose Source method: isolated from a genetically manipulated source | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose / 6alpha-alpha-mannobiose | #6: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-SIA / #9: Sugar | ChemComp-MAN / #10: Sugar | ChemComp-NAG / #13: Sugar | ChemComp-BMA / | |
-Non-polymers , 4 types, 1574 molecules
#8: Chemical | ChemComp-CA / #11: Chemical | ChemComp-GOL / #12: Chemical | ChemComp-PEG / | #14: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.86 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 7 / Details: 0.15 M NACL, 20% PEG 3350 AT 293 K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9853 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 15, 2004 / Details: 1.2 METRE LONG SILICON SUBSTRATE, RHODIUM COATED |
Radiation | Monochromator: SILICON 11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9853 Å / Relative weight: 1 |
Reflection | Resolution: 2→33.78 Å / Num. obs: 112032 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 16.63 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.3 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V0Z Resolution: 2→33.71 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.684 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: UNLIKE OTHER VIRAL NEURAMINIDASES SOLVED TO DATE, N6 HAS A FULL TETRAMER IN THE ASYMMETRIC UNIT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.28 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→33.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|