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Yorodumi- PDB-4acy: Selenomethionine derivative of the GH99 endo-alpha-mannosidase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4acy | ||||||
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Title | Selenomethionine derivative of the GH99 endo-alpha-mannosidase from Bacteroides thetaiotaomicron | ||||||
Components | ENDO-ALPHA-MANNOSIDASE | ||||||
Keywords | HYDROLASE / ENDOMANNOSIDASE / GLYCOSIDE HYDROLASE / CAZY / ENZYME-CARBOHYDRATE INTERACTION / MANNOSE / GLYCOSIDASE INHIBITION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACTEROIDES THETAIOTAOMICRON (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 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 | 4acy.cif.gz | 159.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4acy.ent.gz | 132.1 KB | Display | PDB format |
PDBx/mmJSON format | 4acy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4acy_validation.pdf.gz | 457 KB | Display | wwPDB validaton report |
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Full document | 4acy_full_validation.pdf.gz | 461.6 KB | Display | |
Data in XML | 4acy_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 4acy_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/4acy ftp://data.pdbj.org/pub/pdb/validation_reports/ac/4acy | HTTPS FTP |
-Related structure data
Related structure data | 4aczC 4ad0C 4ad1C 4ad2C 4ad3C 4ad4C 4ad5C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43638.582 Da / Num. of mol.: 2 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-GOL / #3: Chemical | #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: 2.4 Å3/Da / Density % sol: 49.2 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 0.25 M NH4CL, 20% W/V PEG 3350, 0.1 M MES PH 6.5, 5 MM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 17, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 81218 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.9 / % possible all: 91.8 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.69→73.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.83 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.1 / 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: 21.241 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→73.82 Å
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