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Yorodumi- PDB-2ww1: Structure of the Family GH92 Inverting Mannosidase BT3990 from Ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ww1 | |||||||||
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Title | Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 in complex with Thiomannobioside | |||||||||
Components | PUTATIVE ALPHA-1,2-MANNOSIDASE | |||||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE FAMILY 92 / GH92 / BT3990 | |||||||||
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: 2.25 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 | 2ww1.cif.gz | 604.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ww1.ent.gz | 498.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ww1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/2ww1 ftp://data.pdbj.org/pub/pdb/validation_reports/ww/2ww1 | HTTPS FTP |
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-Related structure data
Related structure data | 2wvxSC 2wvyC 2wvzC 2ww0C 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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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 3 / Auth seq-ID: 22 - 750 / Label seq-ID: 3 - 731
NCS oper: (Code: given) |
-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 22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER / References: UniProt: Q8A0N1 #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.: 4 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: Water | ChemComp-HOH / | Nonpolymer details | METHYL-2-S-(ALPHA-D-MANNOPYRAN | Sequence details | FIRST 19 RESIDUES WERE REMOVED DURING CLONING | |
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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: 2.75 Å3/Da / Density % sol: 55.4 % / Description: NONE |
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Crystal grow | Details: 20% 3350 PEG, 0.1 M (4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID) (PH 7.0), 0.15 M K2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→44.6 Å / Num. obs: 174544 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WVX Resolution: 2.25→185.16 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.86 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE ONLY. U VALUES RESIDUAL ONLY
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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: 13.722 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→185.16 Å
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Refine LS restraints |
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