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Yorodumi- PDB-2wvz: Structure of the Family GH92 Inverting Mannosidase BT3990 from Ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wvz | ||||||
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Title | Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 | ||||||
Components | PUTATIVE ALPHA-1,2-MANNOSIDASE | ||||||
Keywords | HYDROLASE / GH92 / BT3990 / GLYCOSIDE HYDROLASE FAMILY 92 | ||||||
Function / homology | Function and homology information peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / glycoprotein catabolic process / protein quality control for misfolded or incompletely synthesized proteins / carbohydrate binding / carbohydrate metabolic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | BACTEROIDES THETAIOTAOMICRON (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Suits, M.D.L. / Zhu, Y. / Thompson, A. / Gilbert, H.J. / Davies, G.J. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2010 Title: Mechanistic Insights Into a Ca2+-Dependent Family of A-Mannosidases in a Human Gut Symbiont. Authors: Zhu, Y. / Suits, M.D.L. / Thompson, A. / Chavan, S. / Dinev, Z. / Dumon, C. / Smith, N. / Moremen, K.W. / Xiang, Y. / Siriwardena, A. / Williams, S.J. / Gilbert, H.J. / 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 | 2wvz.cif.gz | 601.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wvz.ent.gz | 492.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/2wvz ftp://data.pdbj.org/pub/pdb/validation_reports/wv/2wvz | HTTPS FTP |
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-Related structure data
Related structure data | 2wvxSC 2wvyC 2ww0C 2ww1C 2ww2C 2ww3C 2wzsC 2wx8 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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Unit cell |
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-Components
#1: Protein | Mass: 85690.859 Da / Num. of mol.: 4 / Fragment: RESIDUES 20-755 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Strain: VPI-5482 / Plasmid: PET 21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A0N1 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-KIF / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Nonpolymer details | 5-(HYDROXYMET | Sequence details | CLONED WITHOUT FIRST 19 RESIDUES | |
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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: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | Details: 20% V/V 3350, 100MM MIBS BUFFER (PH 6.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→60 Å / Num. obs: 156201 / % possible obs: 88.4 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.1 / % possible all: 89.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WVX Resolution: 2.4→191.14 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.963 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.457 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
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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: 32.364 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→191.14 Å
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Refine LS restraints |
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