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- PDB-1png: CRYSTAL STRUCTURE OF PEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL) ... -

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Basic information

Entry
Database: PDB / ID: 1png
TitleCRYSTAL STRUCTURE OF PEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL) ASPARAGINE AMIDASE AT 2.2 ANGSTROMS RESOLUTION
ComponentsPEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL)ASPARAGINE AMIDASE F
KeywordsHYDROLASE
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: 2.2 Å
AuthorsVan Roey, P. / Kuhn, P.
Citation
Journal: Biochemistry / Year: 1994
Title: Crystal structure of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F at 2.2-A resolution.
Authors: Kuhn, P. / 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 (Pngasef)
Authors: Kuhn, P. / Tarentino, A.L. / Plummer Junior, T.H. / Van Roey, P.
History
DepositionJun 2, 1994Processing site: BNL
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,8161
Polymers34,8161
Non-polymers00
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.160, 125.100, 79.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: CIS PROLINE - PRO 196 / 2: CIS PROLINE - PRO 241 / 3: RESIDUES CYS 204 - ALA 205 FORM A CIS PEPTIDE.

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Components

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


Mass: 34815.852 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.: 222 / Source method: isolated from a natural source / Formula: H2O
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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 4.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.7 mg/mlprotein1drop
25.6 mMcacodylate1drop
31.1 mMdithiothreitol1drop
40.13 Mammonium sulfate1drop
513.3 %PEG33501drop
60.04 Msodium acetate1drop
70.4 Mammonium sulfate1reservoir
832 %PEG33501reservoir
90.1 Msodium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 22074 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Num. measured all: 95693 / Rmerge F obs: 0.056

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Processing

RefinementResolution: 2.2→49.1 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.183 --
obs-21034 93.5 %
Refinement stepCycle: LAST / Resolution: 2.2→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 0 222 2655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.013
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.97
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d1.97
X-RAY DIFFRACTIONo_dihedral_angle_d27.5
X-RAY DIFFRACTIONo_dihedral_angle_deg1.79

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