[English] 日本語
![](img/lk-miru.gif)
- PDB-1pgs: THE THREE-DIMENSIONAL STRUCTURE OF PNGASE F, A GLYCOSYLASPARAGINA... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1pgs | ||||||
---|---|---|---|---|---|---|---|
Title | THE THREE-DIMENSIONAL STRUCTURE OF PNGASE F, A GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM | ||||||
![]() | PEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL)ASPARAGINE AMIDASE F | ||||||
![]() | ENDOGLYCOSIDASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() | ||||||
![]() | Norris, G.E. / Stillman, T.J. / Anderson, B.F. / Baker, E.N. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 77.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 58.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 424.9 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 23.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
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.) ![]() References: UniProt: P21163, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase |
---|---|
#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: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.17 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
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 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→20 Å / σ(F): 0 /
| ||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
| ||||||||||||
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
|