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- PDB-3ljq: Crystal Structure of the Glycosylasparaginase T152C apo-precursor -

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Basic information

Entry
Database: PDB / ID: 3ljq
TitleCrystal Structure of the Glycosylasparaginase T152C apo-precursor
ComponentsN(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
KeywordsHYDROLASE / Aspartylglucosylaminase / Active Precursors / Precursor structure / reversible inhibitor / constrained conformation / Autoproteolysis / catalytic mechanism / N-terminal nucleophile hydrolases
Function / homology
Function and homology information


N4-(beta-N-acetylglucosaminyl)-L-asparaginase / N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity / asparaginase activity / beta-aspartyl-peptidase activity / periplasmic space / lysosome / proteolysis
Similarity search - Function
Peptidase T2, asparaginase 2 / Asparaginase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
GLYCINE / N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
Similarity search - Component
Biological speciesFlavobacterium meningosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, Y. / Guo, H.-C.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystallographic snapshot of glycosylasparaginase precursor poised for autoprocessing.
Authors: Wang, Y. / Guo, H.C.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
C: N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2855
Polymers65,1642
Non-polymers1213
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-22 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.061, 52.533, 61.933
Angle α, β, γ (deg.)81.47, 90.21, 104.93
Int Tables number1
Space group name H-MP1

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Components

#1: Protein N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase / Glycosylasparaginase / Aspartylglucosaminidase / AGA / N4-(N-acetyl-beta-glucosaminyl)-L-asparagine ...Glycosylasparaginase / Aspartylglucosaminidase / AGA / N4-(N-acetyl-beta-glucosaminyl)-L-asparagine amidase / Glycosylasparaginase alpha chain / Glycosylasparaginase beta chain


Mass: 32582.053 Da / Num. of mol.: 2 / Fragment: UNP residues 46-340 / Mutation: T152C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium meningosepticum (bacteria)
Gene: GA(1-295) / Plasmid: pMAL-c2x / Production host: Escherichia coli (E. coli) / Strain (production host): BP-1
References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 277 K / pH: 7.5
Details: 15% PEG 3350, 100 mM HEPES pH 7.5, 0.1% sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.10005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10005 Å / Relative weight: 1
ReflectionResolution: 1.9→31.74 Å / Num. obs: 42606 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.029 / Rsym value: 0.029 / Net I/σ(I): 26.7
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.059 / Mean I/σ(I) obs: 13.3 / Rsym value: 0.059

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 9GAC

9gac


Resolution: 1.9→31.74 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.197 -RANDOM
Rwork0.154 --
obs0.154 42606 -
Refinement stepCycle: LAST / Resolution: 1.9→31.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4323 0 7 512 4842
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.62
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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