[English] 日本語
Yorodumi- PDB-4cpm: Structure of the Neuraminidase from the B/Brisbane/60/2008 virus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cpm | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the Neuraminidase from the B/Brisbane/60/2008 virus in complex with Oseltamivir | |||||||||
Components | NEURAMINIDASE | |||||||||
Keywords | HYDROLASE / VIRAL PROTEIN / OSELTAMIVIR | |||||||||
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 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | INFLUENZA B VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | |||||||||
Authors | Vachieri, S.G. / Collins, P.J. / Escuret, V. / Casalegno, J.S. / Cattle, N. / Ferraris, O. / Sabatier, M. / Frobert, E. / Caro, V. / Skehel, J.J. ...Vachieri, S.G. / Collins, P.J. / Escuret, V. / Casalegno, J.S. / Cattle, N. / Ferraris, O. / Sabatier, M. / Frobert, E. / Caro, V. / Skehel, J.J. / Gamblin, S.J. / Valla, F. / Valette, M. / Ottmann, M. / McCauley, J.W. / Daniels, R.S. / Lina, B. | |||||||||
Citation | Journal: J.Infect.Dis. / Year: 2014 Title: A Novel I221 L Substitution in Neuraminidase Confers High Level Resistance to Oseltamivir in Influenza B Viruses. Authors: Escuret, V. / Collins, P.J. / Casalegno, J. / Vachieri, S.G. / Cattle, N. / Ferraris, O. / Sabatier, M. / Frobert, E. / Caro, V. / Skehel, J.J. / Gamblin, S. / Valla, F. / Valette, M. / ...Authors: Escuret, V. / Collins, P.J. / Casalegno, J. / Vachieri, S.G. / Cattle, N. / Ferraris, O. / Sabatier, M. / Frobert, E. / Caro, V. / Skehel, J.J. / Gamblin, S. / Valla, F. / Valette, M. / Ottmann, M. / Mccauley, J.W. / Daniels, R.S. / Lina, B. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4cpm.cif.gz | 328.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4cpm.ent.gz | 266.6 KB | Display | PDB format |
PDBx/mmJSON format | 4cpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cpm_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4cpm_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4cpm_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 4cpm_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/4cpm ftp://data.pdbj.org/pub/pdb/validation_reports/cp/4cpm | HTTPS FTP |
-Related structure data
Related structure data | 4cplSC 4cpnC 4cpoC 4cpyC 4cpzC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 51182.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) INFLUENZA B VIRUS (B/BRISBANE/60/2008) / References: UniProt: C0LT34, exo-alpha-sialidase |
---|
-Sugars , 3 types, 5 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 |
---|---|
#3: 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: Sugar |
-Non-polymers , 4 types, 104 molecules
#4: Chemical | #6: Chemical | #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.11 % / Description: NONE |
---|---|
Crystal grow | Details: 25% PEG 1500, 0.1M SUCCINIC ACID PH 9.0. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→45.2 Å / Num. obs: 32059 / % possible obs: 93.3 % / Observed criterion σ(I): 1.7 / Redundancy: 2.4 % / Biso Wilson estimate: 50.21 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.7 / % possible all: 96.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CPL Resolution: 2.75→45.204 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 23.44 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→45.204 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|