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Open data
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Basic information
Entry | Database: PDB / ID: 2epm | ||||||
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Title | N-acetyl-B-D-glucoasminidase (GCNA) from Stretococcus gordonii | ||||||
![]() | N-acetyl-beta-D-glucosaminidase | ||||||
![]() | HYDROLASE / glycoside hydrolase / family 20 / glucosaminidase / gcna | ||||||
Function / homology | ![]() beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Langley, D.B. / Harty, D.W.S. / Guss, J.M. / Collyer, C.A. | ||||||
![]() | ![]() Title: Structure of N-acetyl-beta-D-glucosaminidase (GcnA) from the Endocarditis Pathogen Streptococcus gordonii and its Complex with the Mechanism-based Inhibitor NAG-thiazoline Authors: Langley, D.B. / Harty, D.W.S. / Jacques, N.A. / Hunter, N. / Guss, J.M. / Collyer, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.9 KB | Display | ![]() |
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PDB format | ![]() | 106.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.2 KB | Display | ![]() |
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Full document | ![]() | 456.8 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2epkC ![]() 2eplSC ![]() 2epnC ![]() 2epoC C: citing same article ( S: Starting model for refinement |
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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: 72331.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-HG / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 100mM Tris, 1.9M ammonium sulphate, 0.5%(v/v) PEG400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 12, 2006 / Details: Osmic mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→14.95 Å / Num. all: 72240 / Num. obs: 71742 / % possible obs: 99.31 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 8.1 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.04→2.09 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.74 / % possible all: 94.31 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2EPL Resolution: 2.04→14.95 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.449 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.135 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.635 Å2
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Refine analyze | Luzzati coordinate error obs: 0.097 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→14.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.092 Å / Total num. of bins used: 20
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