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Yorodumi- PDB-4ad0: Structure of the GH99 endo-alpha-mannosidase from Bacteriodes the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ad0 | ||||||
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Title | Structure of the GH99 endo-alpha-mannosidase from Bacteriodes thetaiotaomicron in complex with BIS-TRIS-Propane | ||||||
Components | ENDO-ALPHA-MANNOSIDASE | ||||||
Keywords | HYDROLASE / ENDOMANNOSIDASE / GLYCOSIDE HYDROLASE GH99 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / MANNOSE GLYCOSIDASE INHIBITION | ||||||
Function / homology | Glycosyl hydrolase family 99 / Glycosyl hydrolase family 99 / alpha-mannosidase activity / Glycosidases / TIM Barrel / Alpha-Beta Barrel / membrane / Alpha Beta / Endo-alpha-mannosidase Function and homology information | ||||||
Biological species | BACTEROIDES THETAIOTAOMICRON (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 | 4ad0.cif.gz | 265.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ad0.ent.gz | 214.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ad0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ad0_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4ad0_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4ad0_validation.xml.gz | 49.3 KB | Display | |
Data in CIF | 4ad0_validation.cif.gz | 66.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/4ad0 ftp://data.pdbj.org/pub/pdb/validation_reports/ad/4ad0 | HTTPS FTP |
-Related structure data
Related structure data | 4acySC 4aczC 4ad1C 4ad2C 4ad3C 4ad4C 4ad5C 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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Unit cell |
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-Components
#1: Protein | Mass: 43263.426 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Strain: VPI-5482 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q8A109, glycoprotein endo-alpha-1,2-mannosidase #2: Chemical | ChemComp-B3P / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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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: 2.07 Å3/Da / Density % sol: 40.71 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.2 M NABR, 20% W/V PEG 3350, 0.1 M BIS-TRIS PROPANE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 4, 2009 / Details: MIRRORS | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 63710 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.6 | |||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ACY Resolution: 2.09→48.18 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.405 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.047 / 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: 25.846 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→48.18 Å
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Refine LS restraints |
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