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Yorodumi- PDB-2wvy: STRUCTURE OF THE FAMILY GH92 INVERTING MANNOSIDASE BT2199 FROM BA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wvy | ||||||
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Title | STRUCTURE OF THE FAMILY GH92 INVERTING MANNOSIDASE BT2199 FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 | ||||||
Components | 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 / cytosol Similarity search - Function | ||||||
Biological species | BACTEROIDES THETAIOTAOMICRON (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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 | 2wvy.cif.gz | 450.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wvy.ent.gz | 368.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/2wvy ftp://data.pdbj.org/pub/pdb/validation_reports/wv/2wvy | HTTPS FTP |
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-Related structure data
Related structure data | 2wvxSC 2wvzC 2ww0C 2ww1C 2ww2C 2ww3C 2wzsC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 83742.734 Da / Num. of mol.: 3 / Fragment: RESIDUES 22-758 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: Q8A5N9 #2: Water | ChemComp-HOH / | Sequence details | FIRST 21 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: 2.84 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | Details: 10% V/V 2-METHYL-2, 4-PENTANEDIOL, 1.2 M C3H2O4NA2 AND 0.1M 1, 3-BIS(TRIS(HYDROXYMETHYL)METHYLAMINO)PROPANETE (PH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 6, 2008 |
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→60 Å / Num. obs: 139549 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WVX Resolution: 2.26→115.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 10.785 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.181 / 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. DISORDERED REGIONS WERE MODELED BASED ON THE BT2199 SWAINSONINE COMPLEXED STRUCTURE.
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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: 16.105 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→115.47 Å
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Refine LS restraints |
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