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Yorodumi- PDB-2wvx: Structure of the Family GH92 Inverting Mannosidase BT3990 from Ba... -
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-Basic information
Entry | Database: PDB / ID: 2wvx | ||||||
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Title | Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 | ||||||
Components | (PUTATIVE ALPHA-1,2-MANNOSIDASE) x 2 | ||||||
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 / carbohydrate binding / carbohydrate metabolic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | BACTEROIDES THETAIOTAOMICRON (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 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 | 2wvx.cif.gz | 625.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wvx.ent.gz | 534 KB | Display | PDB format |
PDBx/mmJSON format | 2wvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wvx_validation.pdf.gz | 478.6 KB | Display | wwPDB validaton report |
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Full document | 2wvx_full_validation.pdf.gz | 518.2 KB | Display | |
Data in XML | 2wvx_validation.xml.gz | 120 KB | Display | |
Data in CIF | 2wvx_validation.cif.gz | 177.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/2wvx ftp://data.pdbj.org/pub/pdb/validation_reports/wv/2wvx | HTTPS FTP |
-Related structure data
Related structure data | 2wvyC 2wvzC 2ww0C 2ww1C 2ww2C 2ww3C 2wzsC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 86957.078 Da / Num. of mol.: 3 / 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: Protein | | Mass: 86971.109 Da / Num. of mol.: 1 / 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 #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | N-TERMINAL 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: 1.99 Å3/Da / Density % sol: 50.6 % / Description: INITIAL BUILD WITH RESOLVE |
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Crystal grow | Details: 100MM MIBS BUFFER (PH 6.0), 10% V/V PEG 3.35K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 25, 2008 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.3 Å / Num. obs: 248657 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5 / % possible all: 96.6 |
-Processing
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.9→133.63 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.811 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS 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: 8.621 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→133.63 Å
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Refine LS restraints |
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