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Yorodumi- PDB-2c4l: Structure of Neuraminidase Subtype N9 Complexed with 30 MM Sialic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c4l | |||||||||
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Title | Structure of Neuraminidase Subtype N9 Complexed with 30 MM Sialic Acid (NANA, NEU5AC), Crystal Soaked for 24 Hours at 291 K and Finally Backsoaked for 30 Min in a Cryoprotectant Solution which did not contain NEU5AC | |||||||||
Components | NEURAMINIDASE SUBTYPE N9 | |||||||||
Keywords | HYDROLASE / INFLUENZA TYPE A / NEURAMINIDASE / SIALIC ACID / SUBTYPE N9 / GLYCOPROTEIN / GLYCOSIDASE / TRANSMEMBRANE | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.15 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 Influenza Type a Virus Neuraminidase of the N6 Subtype at 1.85 A Resolution Authors: Rudino-Pinera, E. / Crennell, S.J. / Webster, R.G. / Laver, W.G. / Garman, E.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c4l.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c4l.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 2c4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/2c4l ftp://data.pdbj.org/pub/pdb/validation_reports/c4/2c4l | HTTPS FTP |
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-Related structure data
Related structure data | 1v0zC 2c4aC 7nn9S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43723.770 Da / Num. of mol.: 1 / Fragment: RESIDUES 83-470 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/TERN/STERNA ALBIFRONS/N9 / Production host: GALLUS GALLUS (chicken) / References: UniProt: P03472, exo-alpha-sialidase |
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-Sugars , 4 types, 13 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose | ||||
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#3: Sugar | #4: Sugar | ChemComp-NAG / #5: Sugar | ChemComp-BMA / |
-Non-polymers , 2 types, 234 molecules
#6: Chemical | ChemComp-CA / |
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#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.15 % |
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Crystal grow | pH: 6.8 Details: PROTEIN WAS CRYSTALLISED FROM 1.9M POTASSIUM PHOSPHATE PH 6.8, THEN SOAKED FOR 24 HOURS IN 30 MM NEU5AC AND FINALLY BACKSOAKED FOR 30 MIN IN A CRYOPROTECTANT SOLUTION WHICH DID NOT CONTAIN NEU5AC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 11, 2004 / Details: CONFOCAL OSMIC BLUE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→42.7 Å / Num. obs: 27820 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 19.68 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 7NN9 Resolution: 2.15→42.7 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.385 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→42.7 Å
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