+Open data
-Basic information
Entry | Database: PDB / ID: 2xm2 | ||||||
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Title | BtGH84 in complex with LOGNAc | ||||||
Components | O-GLCNACASE BT_4395 | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / INHIBITOR | ||||||
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: 1.95 Å | ||||||
Authors | He, Y. / Davies, G.J. | ||||||
Citation | Journal: Amino Acids / Year: 2011 Title: Inhibition of a Bacterial O-Glcnacase Homologue by Lactone and Lactam Derivatives: Structural, Kinetic and Thermodynamic Analyses. Authors: He, Y. / Bubb, A.K. / Stubbs, K.A. / Gloster, T.M. / Davies, G.J. | ||||||
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 | 2xm2.cif.gz | 554.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xm2.ent.gz | 459.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/2xm2 ftp://data.pdbj.org/pub/pdb/validation_reports/xm/2xm2 | HTTPS FTP |
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-Related structure data
Related structure data | 2xm1C 2choS 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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1 |
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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: Sugar | #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: 2.72 Å3/Da / Density % sol: 54.78 % / Description: NONE |
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Crystal grow | Details: 0.3M AMMONIUM ACETATE, 0.1M MES PH6.0, 15% PEG3350(W/V), 10% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9804 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9804 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→44.65 Å / Num. obs: 119746 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.3 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CHO Resolution: 1.95→43.7 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.447 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.639 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→43.7 Å
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Refine LS restraints |
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