+Open data
-Basic information
Entry | Database: PDB / ID: 2w67 | ||||||
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Title | BtGH84 in complex with FMA34 | ||||||
Components | O-GLCNACASE BT_4395 | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / COMPLEX / INHIBITOR / GLYCOSIDASE | ||||||
Function / homology | Function and homology information protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / identical protein binding Similarity search - Function | ||||||
Biological species | BACTEROIDES THETAIOTAOMICRON VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | He, Y. / Davies, G.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Molecular Basis for Inhibition of Gh84 Glycoside Hydrolases by Substituted Azepanes: Conformational Flexibility Enables Probing of Substrate Distortion. Authors: Marcelo, F. / He, Y. / Yuzwa, S.A. / Nieto, L. / Jimenez-Barbero, J. / Sollogoub, M. / Vocadlo, D.J. / Davies, G.J. / Bleriot, Y. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w67.cif.gz | 266.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w67.ent.gz | 213 KB | Display | PDB format |
PDBx/mmJSON format | 2w67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w67_validation.pdf.gz | 469.3 KB | Display | wwPDB validaton report |
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Full document | 2w67_full_validation.pdf.gz | 485.6 KB | Display | |
Data in XML | 2w67_validation.xml.gz | 48.5 KB | Display | |
Data in CIF | 2w67_validation.cif.gz | 70 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/2w67 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/2w67 | HTTPS FTP |
-Related structure data
Related structure data | 2w66C 2vvnS 2vw3 S: Starting model for refinement 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: 82316.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON VPI-5482 (bacteria) Plasmid: YSBLLICPET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q89ZI2, beta-N-acetylhexosaminidase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: 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: 2.75 Å3/Da / Density % sol: 55.23 % / Description: NONE |
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Crystal grow | Details: 0.3M NH4AC 10% GLYCEROL 15% PEG3350 0.1M MES PH6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 9, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→87.71 Å / Num. obs: 75364 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.5 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VVN Resolution: 2.25→87.71 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.686 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
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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: 20.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→87.71 Å
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Refine LS restraints |
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