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- PDB-1pgs: THE THREE-DIMENSIONAL STRUCTURE OF PNGASE F, A GLYCOSYLASPARAGINA... -

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Entry
Database: PDB / ID: 1pgs
TitleTHE THREE-DIMENSIONAL STRUCTURE OF PNGASE F, A GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM
ComponentsPEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL)ASPARAGINE AMIDASE F
KeywordsENDOGLYCOSIDASE
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
: / Peptide-N-glycosidase F, C-terminal / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, C terminal / Jelly Rolls - #230 / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Peptide-N(4)-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsNorris, 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
DepositionOct 6, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL)ASPARAGINE AMIDASE F


Theoretical massNumber of molelcules
Total (without water)34,8461
Polymers34,8461
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.070, 85.140, 48.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: 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.

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Components

#1: Protein PEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL)ASPARAGINE AMIDASE F


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE 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.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity 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
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.1 MTris-HCl1drop
312 %PEG40001drop
40.1 MTris-HCl1reservoir
518 %(w/v)PEG40001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative 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 %

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.8→20 Å / σ(F): 0 /
RfactorNum. reflection
obs0.168 27995
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 0 230 2667
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg1.9

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