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- PDB-2gl9: Crystal Structure of Glycosylasparaginase-Substrate Complex -

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Basic information

Entry
Database: PDB / ID: 2gl9
TitleCrystal Structure of Glycosylasparaginase-Substrate Complex
Components
  • Glycosylasparaginase alpha chain
  • Glycosylasparaginase beta chain
KeywordsHYDROLASE / glycosylasparaginase / enzyme-substrate complex / catalytic mechanism / proton-relay network / electron-pair transfer / nucleophilic attack / oxyanion hole / enzyme-acyl intermediate / Ntn-hydrolase
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
(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
ASPARAGINE / N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, Y. / Guo, H.C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystallographic snapshot of a productive glycosylasparaginase-substrate complex.
Authors: Wang, Y. / Guo, H.C.
History
DepositionApr 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 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: Glycosylasparaginase alpha chain
B: Glycosylasparaginase beta chain
C: Glycosylasparaginase alpha chain
D: Glycosylasparaginase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1068
Polymers64,3994
Non-polymers7074
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14670 Å2
ΔGint-97 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.118, 96.745, 61.998
Angle α, β, γ (deg.)90.00, 90.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycosylasparaginase alpha chain


Mass: 16819.072 Da / Num. of mol.: 2 / Fragment: residues 46-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Plasmid: pMAL-c2 / Production host: Escherichia coli (E. coli) / Strain (production host): TB1
References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase
#2: Protein Glycosylasparaginase beta chain


Mass: 15380.615 Da / Num. of mol.: 2 / Fragment: residues 197-340 / Mutation: T152C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Plasmid: pMAL-c2 / Production host: Escherichia coli (E. coli) / Strain (production host): TB1
References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 3350, 100 mM HEPES, 0.1% sodium azide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 17, 2003
RadiationMonochromator: confocal optical system (blue configuration) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→17.35 Å / Num. all: 39759 / Num. obs: 39436 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 14.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3753 / Rsym value: 0.337 / % possible all: 94.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SCALEPACKdata scaling
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GAC

2gac


Resolution: 2→17.35 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: CNS bulk solvent model used
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2964 -RANDOM
Rwork0.17 ---
all0.174 36691 --
obs0.174 36634 99.8 %-
Displacement parametersBiso mean: 19.95 Å2
Baniso -1Baniso -2Baniso -3
1--4.74 Å20 Å2-0.05 Å2
2--4.49 Å20 Å2
3---0.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→17.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 47 377 4770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.05
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.279 383 -
Rwork0.217 --
obs-4540 99.4 %

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