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Yorodumi- PDB-2ber: Y370G Active Site Mutant of the Sialidase from Micromonospora vir... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ber | ||||||
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Title | Y370G Active Site Mutant of the Sialidase from Micromonospora viridifaciens in complex with beta-Neu5Ac (sialic acid). | ||||||
Components | BACTERIAL SIALIDASE | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / SIALIDASE / BETA-PROPELLER / MICROMONOSPORA VIRIDIFACIENS | ||||||
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: 1.8 Å | ||||||
Authors | Newstead, S. / Watson, J.N. / Bennet, A.J. / Taylor, G.L. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structure and Mechanism of Action of an Inverting Mutant Sialidase. Authors: Newstead, S. / Watson, J.N. / Knoll, T.L. / Bennet, A.J. / Taylor, G.L. | ||||||
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 | 2ber.cif.gz | 148.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ber.ent.gz | 112.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ber.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/2ber ftp://data.pdbj.org/pub/pdb/validation_reports/be/2ber | HTTPS FTP |
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-Related structure data
Related structure data | 1w8oS 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
#1: Protein | Mass: 64192.504 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: Sugar | ChemComp-SLB / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.4 % |
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Crystal grow | pH: 5 / Details: 16 % PEG 3350, 0.2 M SODIUM FLUORIDE., pH 5.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 23, 2004 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→34.94 Å / Num. obs: 53080 / % possible obs: 87.3 % / Observed criterion σ(I): 6 / Redundancy: 2.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.1 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W8O Resolution: 1.8→105.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.499 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.134 / 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: 13.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→105.41 Å
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Refine LS restraints |
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