+Open data
-Basic information
Entry | Database: PDB / ID: 3pt5 | ||||||
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Title | Crystal structure of NanS | ||||||
Components | NANS (YJHS), A 9-O-acetyl N-acetylneuraminic acid esterase | ||||||
Keywords | HYDROLASE / SGNH hydrolase / 9-O-acetyl N-acetylneuraminic acid esterase / Structural genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI | ||||||
Function / homology | Sialate O-acetylesterase domain / Carbohydrate esterase, sialic acid-specific acetylesterase / SGNH hydrolase superfamily / hydrolase activity / Sialate O-acetylesterase / Sialate O-acetylesterase Function and homology information | ||||||
Biological species | Escherichia coli O157:H7 EDL933 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Ruane, K.M. / Rangarajan, E.S. / Proteau, A. / Schrag, J.D. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: Structural and enzymatic characterization of NanS (YjhS), a 9-O-Acetyl N-acetylneuraminic acid esterase from Escherichia coli O157:H7. Authors: Rangarajan, E.S. / Ruane, K.M. / Proteau, A. / Schrag, J.D. / Valladares, R. / Gonzalez, C.F. / Gilbert, M. / Yakunin, A.F. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pt5.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pt5.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pt5_validation.pdf.gz | 421.5 KB | Display | wwPDB validaton report |
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Full document | 3pt5_full_validation.pdf.gz | 423.4 KB | Display | |
Data in XML | 3pt5_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 3pt5_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/3pt5 ftp://data.pdbj.org/pub/pdb/validation_reports/pt/3pt5 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38127.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 EDL933 (bacteria) Strain: O157:H7 EDL933 / Gene: ECs5268, YjhS / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7A8N3, UniProt: A0A0H3JKI3*PLUS |
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#2: 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: 2.11 Å3/Da / Density % sol: 41.77 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5, 30% (w/v) PEG 3350, vapor diffusion, sitting drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97923 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: Mar225 / Detector: CCD / Date: May 15, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 40446 / % possible obs: 92.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33.84 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.098 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.489 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→33.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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