[English] 日本語
Yorodumi- PDB-2ww3: Structure of the Family GH92 Inverting Mannosidase BT3990 from Ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ww3 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
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: 2.1 Å | |||||||||
Authors | Suits, M.D.L. / Zhu, Y. / Thompson, A.J. / Gilbert, H.J. / Davies, G.J. | |||||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2010 Title: Mechanistic Insights Into a Ca(2+)-Dependent Family of Alpha-Mannosidases in a Human Gut Symbiont. Authors: Zhu, Y. / Suits, M.D.L. / Thompson, A.J. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ww3.cif.gz | 880.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ww3.ent.gz | 729.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ww3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/2ww3 ftp://data.pdbj.org/pub/pdb/validation_reports/ww/2ww3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2wvxSC 2wvyC 2wvzC 2ww0C 2ww1C 2ww2C 2wzsC 2wx8 C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 85690.859 Da / Num. of mol.: 6 / 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.: 6 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 | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL)-2-THIO- ALPHA-D-MANNOPYRANOSIDE (SMD): ALPHA-1,2 SULPHUR LINKED ...METHYL-2-S-(ALPHA-D-MANNOPYRAN | Sequence details | FIRST 19 RESIDUES WERE REMOVED DURING CLONING | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.3 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 239524 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 95.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WVX Resolution: 2.1→203.33 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 13.377 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 27.262 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→203.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|