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Yorodumi- PDB-4ad1: Structure of the GH99 endo-alpha-mannosidase from Bacteroides xyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ad1 | ||||||
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Title | Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens | ||||||
Components | GLYCOSYL HYDROLASE FAMILY 71 | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE GH99 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / MANNOSE GLYCOSIDASE INHIBITION | ||||||
Function / homology | Glycosyl hydrolase family 99 / Glycosyl hydrolase family 99 / hydrolase activity, acting on glycosyl bonds / Glycosidases / TIM Barrel / Alpha-Beta Barrel / membrane / Alpha Beta / Glycosyl hydrolase family 71 Function and homology information | ||||||
Biological species | BACTEROIDES XYLANISOLVENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ad1.cif.gz | 92.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ad1.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ad1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/4ad1 ftp://data.pdbj.org/pub/pdb/validation_reports/ad/4ad1 | HTTPS FTP |
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-Related structure data
Related structure data | 4acyC 4aczC 4ad0C 4ad2C 4ad3C 4ad4C 4ad5C C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 43479.266 Da / Num. of mol.: 1 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.04 % / Description: NONE |
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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: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 30, 2011 / Details: OSMICS MULTILAYER OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 31100 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 8.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PREVIOUSLY SOLVED STRUCTURE OF CLOSELY RELATED HOMOLOG Resolution: 1.9→38.37 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.337 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 14.696 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→38.37 Å
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Refine LS restraints |
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