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Yorodumi- PDB-1w8o: Contribution of the Active Site Aspartic Acid to Catalysis in the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w8o | |||||||||
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Title | Contribution of the Active Site Aspartic Acid to Catalysis in the Bacterial Neuraminidase from Micromonospora viridifaciens | |||||||||
Components | BACTERIAL SIALIDASE | |||||||||
Keywords | HYDROLASE / GLYCOSIDASE / SIALIDASE / BETA-PROPELLER | |||||||||
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 / extracellular region Similarity search - Function | |||||||||
Biological species | MICROMONOSPORA VIRIDIFACIENS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Newstead, S. / Watson, J.N. / Dookhun, V. / Bennet, A.J. / Taylor, G. | |||||||||
Citation | Journal: FEBS Lett. / Year: 2004 Title: Contribution of the Active Site Aspartic Acid to Catalysis in the Bacterial Neuraminidase from Micromonospora Viridifaciens Authors: Watson, J.N. / Newstead, S. / Dookhun, V. / Taylor, G. / Bennet, A.J. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w8o.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w8o.ent.gz | 112 KB | Display | PDB format |
PDBx/mmJSON format | 1w8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/1w8o ftp://data.pdbj.org/pub/pdb/validation_reports/w8/1w8o | HTTPS FTP |
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-Related structure data
Related structure data | 1w8nC 1eutS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 64240.598 Da / Num. of mol.: 1 / Fragment: RESIDUES 47-647 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MICROMONOSPORA VIRIDIFACIENS (bacteria) Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02834, exo-alpha-sialidase |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose |
-Non-polymers , 4 types, 715 molecules
#3: Chemical | ChemComp-CIT / | ||||
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#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 54.9 % |
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Crystal grow | Details: 16 % PEG 3350, 0.2M AMMONIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 12, 2003 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→43.6 Å / Num. obs: 82420 / % possible obs: 92 % / Observed criterion σ(I): 6 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.4 / % possible all: 72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EUT Resolution: 1.7→87.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.702 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→87.71 Å
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Refine LS restraints |
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