+Open data
-Basic information
Entry | Database: PDB / ID: 2epk | ||||||
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Title | N-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii | ||||||
Components | N-acetyl-beta-D-glucosaminidase | ||||||
Keywords | HYDROLASE / glycoside hydrolase / family 20 / gcna / glucosaminidase | ||||||
Function / homology | Function and homology information beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / metabolic process Similarity search - Function | ||||||
Biological species | Streptococcus gordonii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Langley, D.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2epk.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2epk.ent.gz | 110.2 KB | Display | PDB format |
PDBx/mmJSON format | 2epk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/2epk ftp://data.pdbj.org/pub/pdb/validation_reports/ep/2epk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 73034.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus gordonii (bacteria) / Strain: FSS2 / Gene: gcna / Plasmid: pHAR100 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE) / References: UniProt: Q6ST21, beta-N-acetylhexosaminidase | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM HEPES, 2M ammonium sulphate, 0.5 %(v/v) PEG400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97928, 0.97945, 0.94929 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 21, 2006 | ||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→39.97 Å / Num. all: 97867 / Num. obs: 97524 / % possible obs: 99.64 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.4 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.4 | ||||||||||||
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.24 / % possible all: 95.58 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→39.97 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.807 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.11 / ESU R Free: 0.105 / 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: 30.89 Å2
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Refine analyze | Luzzati coordinate error obs: 0.085 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→39.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.849→1.897 Å / Total num. of bins used: 20
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