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- PDB-1p4v: CRYSTAL STRUCTURE OF THE GLYCOSYLASPARAGINASE PRECURSOR D151N MUT... -

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Basic information

Entry
Database: PDB / ID: 1p4v
TitleCRYSTAL STRUCTURE OF THE GLYCOSYLASPARAGINASE PRECURSOR D151N MUTANT WITH GLYCINE
ComponentsN(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase precursor
KeywordsHYDROLASE / ALPHA BETA / BETA ALPHA / SANDWICH
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
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 speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsQian, X. / Guan, C. / Guo, H.C.
CitationJournal: Structure / Year: 2003
Title: A dual role for an aspartic acid in glycosylasparaginase autoproteolysis.
Authors: Qian, X. / Guan, C. / Guo, H.C.
History
DepositionApr 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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 precursor
C: N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5074
Polymers64,3572
Non-polymers1502
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-25 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.877, 52.369, 61.741
Angle α, β, γ (deg.)80.92, 90.41, 105.10
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 32178.645 Da / Num. of mol.: 2 / Fragment: Glycosylasparaginase, alpha and beta chains / Mutation: D151N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Plasmid: pMAL-c2x / Production host: Escherichia coli (E. coli)
References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.13 Å3/Da / Density % sol: 41.89 %
Crystal growMethod: evaporation / pH: 7.5
Details: 15% PEG 3300, 0.1M Tris, pH 7.5, 0.2M lithium sulfate, 0.1% sodium azide, 0.05M glycine, EVAPORATION
Crystal grow
*PLUS
Temperature: 283 K / pH: 7.4 / Method: sparse matrix sampling method / Details: Cui, T., (1999) Acta Crystallogr., D55, 1961.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris11pH7.4
250 mM11NaCl
31 mMEDTA11
420 mMglycine11
55 mg/mlprotein11
68 %PEG800012
730 %PEG400012
80.2 Mlithium sulfate12pH8.5
90.1 MTris12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1001 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1001 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 43152 / Num. obs: 43152 / Rsym value: 0.03
Reflection shellResolution: 1.9→1.93 Å / Rsym value: 0.08
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. obs: 41067 / % possible obs: 95.3 % / Num. measured all: 81010 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.225 4080 RANDOM
Rwork0.193 --
all-43125 -
obs-41025 -
Displacement parametersBiso mean: 13.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4510 0 10 212 4732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.4
X-RAY DIFFRACTIONc_bond_d0.006
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.2254 / Rfactor Rwork: 0.1928
Solvent computation
*PLUS
Displacement parameters
*PLUS

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