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- PDB-1ayy: GLYCOSYLASPARAGINASE -

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Basic information

Entry
Database: PDB / ID: 1ayy
TitleGLYCOSYLASPARAGINASE
Components(GLYCOSYLASPARAGINASE) x 2
KeywordsHYDROLASE / GLYCOAMIDASE
Function / homology
Function and homology information


N4-(beta-N-acetylglucosaminyl)-L-asparaginase / N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity / peptidase activity / periplasmic space / proteolysis / cytoplasm
Similarity search - Function
(Glycosyl)asparaginase / Peptidase T2, asparaginase 2 / Asparaginase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT, PHASE COMBINATION WITH 2 DERIVATIVES / Resolution: 2.32 Å
AuthorsVan Roey, P. / Xuan, J.
CitationJournal: Protein Sci. / Year: 1998
Title: Crystal structure of glycosylasparaginase from Flavobacterium meningosepticum.
Authors: Xuan, J. / Tarentino, A.L. / Grimwood, B.G. / Plummer Jr., T.H. / Cui, T. / Guan, C. / Van Roey, P.
History
DepositionNov 12, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOSYLASPARAGINASE
B: GLYCOSYLASPARAGINASE
C: GLYCOSYLASPARAGINASE
D: GLYCOSYLASPARAGINASE


Theoretical massNumber of molelcules
Total (without water)64,3954
Polymers64,3954
Non-polymers00
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14450 Å2
ΔGint-99 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.200, 115.600, 52.400
Angle α, β, γ (deg.)90.00, 107.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GLYCOSYLASPARAGINASE / ASPARTYLGLUCOSAMINIDASE


Mass: 16819.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase
#2: Protein GLYCOSYLASPARAGINASE / ASPARTYLGLUCOSAMINIDASE


Mass: 15378.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS A SINGLE CHAIN PRECURSOR ACTIVATED BY PROTEOLYTIC CLEAVAGE BETWEEN RESIDUES 151 AND 152.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41 %
Crystal growpH: 8.5 / Details: 19% PEG3350 IN 100 MM TRIS.HCL PH 8.5
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15.8 mg/mlprotein1drop
210 mMTris-HCl1drop
35 mM1dropNaCl
41 mMEDTA1drop
519 %PEG33501reservoir
6100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.32→20 Å / Num. obs: 22627 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 7
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 2.73 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3 / Rsym value: 0.17 / % possible all: 72.2

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Processing

Software
NameVersionClassification
AMoREphasing
PHASESphasing
X-PLOR3.8refinement
bioteXdata reduction
bioteXdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, PHASE COMBINATION WITH 2 DERIVATIVES
Starting model: HUMAN GLYCOSYLASPARAGINASE DIMER

Resolution: 2.32→20 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2130 10 %RANDOM
Rwork0.188 ---
obs0.188 22627 95.7 %-
Displacement parametersBiso mean: 26.5 Å2
Refinement stepCycle: LAST / Resolution: 2.32→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4301 0 0 200 4501
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.003
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.895
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.28
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.49
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.32→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3319 234 10 %
Rwork0.1894 1838 -
obs--72.2 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.28
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.49

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