+Open data
-Basic information
Entry | Database: PDB / ID: 1pnf | |||||||||
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Title | PNGASE F COMPLEX WITH DI-N-ACETYLCHITOBIOSE | |||||||||
Components | PEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL)ASPARAGINE AMIDASE F | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity Similarity search - Function | |||||||||
Biological species | Elizabethkingia meningoseptica (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | |||||||||
Authors | Van Roey, P. / Kuhn, P. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1995 Title: Active site and oligosaccharide recognition residues of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F. Authors: Kuhn, P. / Guan, C. / Cui, T. / Tarentino, A.L. / Plummer Jr., T.H. / Van Roey, P. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary Crystallographic Analysis of Peptide-N(4)-(N-Acetyl-Beta-D-Glucosaminyl) Asparagine Amidase (Pngase F) Authors: Kuhn, P. / Tarentino, A.L. / Plummer Junior, T.H. / Van Roey, P. #2: Journal: Biochemistry / Year: 1994 Title: Crystal Structure of Peptide-N(4)-(N-Acetyl-Beta-D-Glucosaminyl) Asparagine Amidase at 2.2 Angstroms Resolution Authors: Kuhn, P. / Tarentino, A.L. / Plummer Junior, T.H. / Van Roey, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pnf.cif.gz | 76.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pnf.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 1pnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/1pnf ftp://data.pdbj.org/pub/pdb/validation_reports/pn/1pnf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 196 2: CYS 204 - ALA 205 OMEGA = 0.37 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: CIS PROLINE - PRO 241 |
-Components
#1: Protein | Mass: 34815.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Elizabethkingia meningoseptica (bacteria) References: UniProt: P21163, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.86 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.96→35 Å / Num. obs: 28801 / % possible obs: 96 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Rmerge(I) obs: 0.044 |
-Processing
Software |
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Refinement | Resolution: 2→10 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |