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Yorodumi- PDB-5g2m: Crystal structure of NagZ from Pseudomonas aeruginosa in complex ... -
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-Basic information
Entry | Database: PDB / ID: 5g2m | ||||||
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Title | Crystal structure of NagZ from Pseudomonas aeruginosa in complex with N-acetylglucosamine | ||||||
Components | BETA-HEXOSAMINIDASEHexosaminidase | ||||||
Keywords | HYDROLASE / CELL-WALL RECYCLING / ANTIBIOTIC RESISTANCE / GLYCOSIDE HYDROLASE / BETA-HEXOSAMINIDASE / PEPTIDOGLYCAN | ||||||
Function / homology | Function and homology information peptidoglycan turnover / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division ...peptidoglycan turnover / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division / response to antibiotic / cytoplasm Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Acebron, I. / Artola-Recolons, C. / Mahasenan, K. / Mobashery, S. / Hermoso, J.A. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Catalytic Cycle of the N-Acetylglucosaminidase NagZ from Pseudomonas aeruginosa. Authors: Acebron, I. / Mahasenan, K.V. / De Benedetti, S. / Lee, M. / Artola-Recolons, C. / Hesek, D. / Wang, H. / Hermoso, J.A. / Mobashery, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g2m.cif.gz | 263.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g2m.ent.gz | 221.4 KB | Display | PDB format |
PDBx/mmJSON format | 5g2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/5g2m ftp://data.pdbj.org/pub/pdb/validation_reports/g2/5g2m | HTTPS FTP |
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-Related structure data
Related structure data | 5g1mC 5g3rC 5g5kC 5g5uC 5g6tC 5ly7C C: citing same article (ref.) |
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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: 38317.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: BOTH PROTEIN CHAINS CONTAIN A HIS RESIDUE AT POSITION -1 FROM THE FUSION TAG USED FOR PURIFICATION Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HZK0, beta-N-acetylhexosaminidase #2: Sugar | Nonpolymer details | N-ACETYL-D-GLUCOSAMINE (NAG): NAG COMES FROM THE HYDROLYSIS OF THE SUBSTRATE NAG-ANHYDROMUR ...N-ACETYL-D-GLUCOSAMIN | Sequence details | THE SEQUENCE CONTAINS A HIS-TAG AT THE N-TERMINUS CONTAINING | |
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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: 2.04 Å3/Da / Density % sol: 39.6 % / Description: NONE |
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Crystal grow | pH: 6 Details: 30% PEG 8000 100 MM SODIUM CACODYLATE PH 6.0 200 MM SODIUM ACETATE PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87292 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2015 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87292 Å / Relative weight: 1 |
Reflection | Resolution: 3→47.33 Å / Num. obs: 13847 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 3.3 % / Biso Wilson estimate: 67.94 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: APO STRUCTURE OF NAGZ FROM PSEUDOMONAS AERUGINOSA Resolution: 3→45.441 Å / SU ML: 0.53 / σ(F): 1.34 / Phase error: 29.19 / Stereochemistry target values: ML Details: RESIDUES 171-173 FROM CHAIN A AND RESIDUES 170-173 FROM CHAIN B ARE NOT IN THE STRUCTURE SINCE THERE ARE NO ELECTRON DENSITY TO FIGURE OUT WHERE THEY REALLY ARE
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→45.441 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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