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Open data
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Basic information
Entry | Database: PDB / ID: 2wca | ||||||
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Title | BtGH84 in complex with n-butyl pugnac | ||||||
![]() | O-GLCNACASE BT_4395 | ||||||
![]() | HYDROLASE / GLYCOSIDE HYDROLASE / COMPLEX / INHIBITOR / GLYCOSIDASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | He, Y. / Davies, G.J. | ||||||
![]() | ![]() Title: Insight Into a Strategy for Attenuating Ampc- Mediated Beta-Lactam Resistance: Structural Basis for Selective Inhibition of the Glycoside Hydrolase Nagz. Authors: Balcewich, M.D. / Stubbs, K.A. / He, Y. / James, T.W. / Davies, G.J. / Vocadlo, D.J. / Mark, B.L. | ||||||
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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.1 KB | Display | ![]() |
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PDB format | ![]() | 104.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 755.8 KB | Display | ![]() |
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Full document | ![]() | 762.1 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gs6C ![]() 3gsmC ![]() 2choS ![]() 2vw3 S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 82316.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: YSBLLICPET28 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-NP6 / [[( |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.68 % / Description: NONE |
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Crystal grow | Details: 15% PEG 3350, 0.5M NH4AC, 0.1M MES PH6.0, 10% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→57.07 Å / Num. obs: 35434 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CHO Resolution: 2.3→46.23 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.056 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.218 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.054 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→46.23 Å
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Refine LS restraints |
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