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Yorodumi- PDB-1pgs: THE THREE-DIMENSIONAL STRUCTURE OF PNGASE F, A GLYCOSYLASPARAGINA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pgs | ||||||
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Title | THE THREE-DIMENSIONAL STRUCTURE OF PNGASE F, A GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM | ||||||
Components | PEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL)ASPARAGINE AMIDASE F | ||||||
Keywords | ENDOGLYCOSIDASE | ||||||
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: 1.8 Å | ||||||
Authors | Norris, G.E. / Stillman, T.J. / Anderson, B.F. / Baker, E.N. | ||||||
Citation | Journal: Structure / Year: 1994 Title: The three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum. Authors: Norris, G.E. / Stillman, T.J. / Anderson, B.F. / Baker, E.N. #1: Journal: To be Published Title: Crystal Structure of Peptide-N(4)-(N-Acetyl-Beta-D-Glucosaminyl)Asparagine Amidase F at 2.2 Angstroms Resolution Authors: Kuhn, P. / Tarantino, A.L. / Plummer Junior, T.H. / Van Roey, P. #2: Journal: J.Biol.Chem. / Year: 1994 Title: Purification and Crystallization of the Endoglycosidase Pgnase F, a Peptide:N-Glycosidase from Flavobacterium Meningosepticum Authors: Norris, G.E. / Flaus, A.J. / Moore, C.H. / Baker, E.N. #3: Journal: J.Biol.Chem. / Year: 1990 Title: Cloning and Expression of Peptide-N4-(N-Acetyl-Beta-D-Glucosaminyl)Asparagine Amidase F in Escherichia Coli Authors: Barsomian, G.D. / Johnson, T.L. / Borowski, M. / Denman, J. / Ollington, J.F. / Hirani, S. / Mcneilly, D.S. / Rasmussen, J.R. #4: Journal: J.Biol.Chem. / Year: 1990 Title: Molecular Cloning and Amino Acid Sequence of Peptide-N4-(N-Acetyl-Beta-D-Glucosaminyl)Asparagine Amidase from Flavobacterium Meningosepticum Authors: Tarentino, A.L. / Quinones, G. / Trumble, A. / Changchien, L.M. / Duceman, B. / Maley, F. / Plummer Junior, T.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pgs.cif.gz | 74.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pgs.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 1pgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/1pgs ftp://data.pdbj.org/pub/pdb/validation_reports/pg/1pgs | 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 = 5.63 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: CIS PROLINE - PRO 241 4: RESIDUE TRP 86 IS THE CENTRAL RESIDUE OF CLASSICAL GAMMA TURN (PHI = 63, PSI = -42). 5: RESIDUES CYS 231 - THR 245 FORM A WIDE OMEGA LOOP. |
-Components
#1: Protein | Mass: 34845.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria) References: UniProt: P21163, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase |
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#2: Water | ChemComp-HOH / |
Compound details | RESIDUE TRP 86 IS THE CENTRAL RESIDUE OF CLASSICAL GAMMA TURN (PHI = 63, PSI = -42). RESIDUES CYS ...RESIDUE TRP 86 IS THE CENTRAL RESIDUE OF CLASSICAL GAMMA TURN (PHI = 63, PSI = -42). RESIDUES CYS 231 - THR 245 FORM A WIDE OMEGA LOOP. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.17 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
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 | *PLUS Highest resolution: 1.8 Å / Num. obs: 28025 / % possible obs: 84.4 % / Observed criterion σ(I): 0 / Num. measured all: 143717 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 2 Å / % possible obs: 65 % |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||
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Refinement | Resolution: 1.8→20 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||
Refinement | *PLUS Num. reflection all: 27995 / Rfactor all: 0.168 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS Biso mean: 19.5 Å2 | ||||||||||||
Refine LS restraints | *PLUS
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