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Yorodumi- PDB-4ayp: Structure of The GH47 processing alpha-1,2-mannosidase from Caulo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ayp | |||||||||
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Title | Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with thiomannobioside | |||||||||
Components | MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE | |||||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / GH47 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / MANNOSE / GLYCOSIDASE INHIBITION / QUANTUM MECHANICS | |||||||||
Function / homology | Function and homology information mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / carbohydrate metabolic process / calcium ion binding / membrane Similarity search - Function | |||||||||
Biological species | CAULOBACTER SP. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 Å | |||||||||
Authors | Thompson, A.J. / Dabin, J. / Iglesias-Fernandez, J. / Iglesias-Fernandez, A. / Dinev, Z. / Williams, S.J. / Siriwardena, A. / Moreland, C. / Hu, T.C. / Smith, D.K. ...Thompson, A.J. / Dabin, J. / Iglesias-Fernandez, J. / Iglesias-Fernandez, A. / Dinev, Z. / Williams, S.J. / Siriwardena, A. / Moreland, C. / Hu, T.C. / Smith, D.K. / Gilbert, H.J. / Rovira, C. / Davies, G.J. | |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2012 Title: The Reaction Coordinate of a Bacterial Gh47 Alpha-Mannosidase: A Combined Quantum Mechanical and Structural Approach. Authors: Thompson, A.J. / Dabin, J. / Iglesias-Fernandez, J. / Ardevol, A. / Dinev, Z. / Williams, S.J. / Bande, O. / Siriwardena, A. / Moreland, C. / Hu, T.C. / Smith, D.K. / Gilbert, H.J. / Rovira, C. / Davies, G.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ayp.cif.gz | 224.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ayp.ent.gz | 177.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ayp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ayp_validation.pdf.gz | 750.3 KB | Display | wwPDB validaton report |
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Full document | 4ayp_full_validation.pdf.gz | 751.8 KB | Display | |
Data in XML | 4ayp_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 4ayp_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/4ayp ftp://data.pdbj.org/pub/pdb/validation_reports/ay/4ayp | HTTPS FTP |
-Related 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: 50546.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CAULOBACTER SP. (bacteria) / Strain: K31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER References: UniProt: B0SWV2, mannosyl-oligosaccharide 1,2-alpha-mannosidase | ||||||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside / methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 372.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: oligosaccharide with S-glycosidic bond between monosaccharides References: methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside | ||||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Sequence details | N-TERMINAL TRUNCATION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.6 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.2 M AMMONIUM ACTETATE, 0.1 M BIS-TRIS PH 6.5, 22% WT/VOL PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7749 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 0.85→46.65 Å / Num. obs: 333281 / % possible obs: 97.2 % / Observed criterion σ(I): 1.7 / Redundancy: 5.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 0.85→0.9 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / % possible all: 80.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PREVIOUSLY SOLVED NATIVE STRUCTURE Resolution: 0.85→39.16 Å / Cor.coef. Fo:Fc: 0.99 / Cor.coef. Fo:Fc free: 0.987 / SU B: 0.232 / SU ML: 0.006 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 8.802 Å2
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Refinement step | Cycle: LAST / Resolution: 0.85→39.16 Å
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Refine LS restraints |
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