[English] 日本語
Yorodumi- PDB-4ad2: Structure of the GH99 endo-alpha-mannosidase from Bacteroides xyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ad2 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with glucose-1,3-isofagomine | ||||||
Components | GLYCOSYL HYDROLASE FAMILY 71 | ||||||
Keywords | HYDROLASE / ENDOMANNOSIDASE / GLYCOSIDE HYDROLASE GH99 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / MANNOSE GLYCOSIDASE INHIBITION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACTEROIDES XYLANISOLVENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Thompson, A.J. / Williams, R.J. / Hakki, Z. / Alonzi, D.S. / Wennekes, T. / Gloster, T.M. / Songsrirote, K. / Thomas-Oates, J.E. / Wrodnigg, T.M. / Spreitz, J. ...Thompson, A.J. / Williams, R.J. / Hakki, Z. / Alonzi, D.S. / Wennekes, T. / Gloster, T.M. / Songsrirote, K. / Thomas-Oates, J.E. / Wrodnigg, T.M. / Spreitz, J. / Stuetz, A.E. / Butters, T.D. / Williams, S.J. / Davies, G.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural and Mechanistic Insight Into N-Glycan Processing by Endo-Alpha-Mannosidase. Authors: Thompson, A.J. / Williams, R.J. / Hakki, Z. / Alonzi, D.S. / Wennekes, T. / Gloster, T.M. / Songsrirote, K. / Thomas-Oates, J.E. / Wrodnigg, T.M. / Spreitz, J. / Stutz, A.E. / Butters, T.D. ...Authors: Thompson, A.J. / Williams, R.J. / Hakki, Z. / Alonzi, D.S. / Wennekes, T. / Gloster, T.M. / Songsrirote, K. / Thomas-Oates, J.E. / Wrodnigg, T.M. / Spreitz, J. / Stutz, A.E. / Butters, T.D. / Williams, S.J. / Davies, G.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ad2.cif.gz | 311.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ad2.ent.gz | 252.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ad2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ad2_validation.pdf.gz | 491.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ad2_full_validation.pdf.gz | 514.7 KB | Display | |
Data in XML | 4ad2_validation.xml.gz | 65.4 KB | Display | |
Data in CIF | 4ad2_validation.cif.gz | 97.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/4ad2 ftp://data.pdbj.org/pub/pdb/validation_reports/ad/4ad2 | HTTPS FTP |
-Related structure data
Related structure data | 4acyC 4aczC 4ad0C 4ad1C 4ad3C 4ad4C 4ad5C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43479.266 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES XYLANISOLVENS (bacteria) / Strain: XB1A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: D6D1V7, glycoprotein endo-alpha-1,2-mannosidase #2: Sugar | ChemComp-GLC / #3: Chemical | ChemComp-IFM / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.3 % / Description: NONE |
---|---|
Crystal grow | pH: 5.5 Details: 0.1 M SODIUM ACETATE PH 4.9, 20% W/V PEG 2000 MME, 1.6% PGA-LM (POLY-GAMMA-GLUTAMIC ACID LOW MOLECULAR WEIGHT) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 140911 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 10 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PREVIOUSLY SOLVED STRUCTURE OF CLOSELY RELATED HOMOLOG Resolution: 2.1→44.36 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.349 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 28.882 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|