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- PDB-6nq6: Structure & function of a new Aspartylglucosaminuria variant -

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Basic information

Entry
Database: PDB / ID: 6nq6
TitleStructure & function of a new Aspartylglucosaminuria variant
Components(N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase) x 2
KeywordsHYDROLASE
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 / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase / Glycosylasparaginase
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPande, S. / Guo, H.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)DK075294 United States
CitationJournal: Protein Sci. / Year: 2019
Title: The T99K variant of glycosylasparaginase shows a new structural mechanism of the genetic disease aspartylglucosaminuria.
Authors: Pande, S. / Guo, H.C.
History
DepositionJan 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
B: N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
C: N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
D: N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase


Theoretical massNumber of molelcules
Total (without water)61,3704
Polymers61,3704
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14330 Å2
ΔGint-91 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.150, 96.020, 61.490
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase


Mass: 15306.469 Da / Num. of mol.: 2 / Mutation: T99K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Gene: NCTC10588_03193 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: A0A376EJJ1, UniProt: A0A494J7W2*PLUS, N4-(beta-N-acetylglucosaminyl)-L-asparaginase
#2: Protein N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase


Mass: 15378.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Gene: NCTC10588_03193 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: A0A376EJJ1, UniProt: A0A494J7W2*PLUS, N4-(beta-N-acetylglucosaminyl)-L-asparaginase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.22 Å3/Da / Density % sol: 44.65 % / Description: Rectangular crystal
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2M NaCl, 0.1M HEPES (pH 7.5), 27% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 80277 / % possible obs: 98.96 % / Redundancy: 2 % / Rsym value: 0.08 / Net I/σ(I): 9.8
Reflection shellResolution: 1.5→1.53 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GL9

2gl9


Resolution: 1.5→19.99 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.504 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22446 4333 5.1 %RANDOM
Rwork0.19429 ---
obs0.19582 80277 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.216 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4228 0 0 162 4390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0194301
X-RAY DIFFRACTIONr_bond_other_d0.0020.024083
X-RAY DIFFRACTIONr_angle_refined_deg2.2141.9525792
X-RAY DIFFRACTIONr_angle_other_deg1.24239468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9865558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79424.787188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36515770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9811526
X-RAY DIFFRACTIONr_chiral_restr0.1970.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024829
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02837
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3781.242229
X-RAY DIFFRACTIONr_mcbond_other1.3551.2392228
X-RAY DIFFRACTIONr_mcangle_it2.011.8522779
X-RAY DIFFRACTIONr_mcangle_other2.011.8532780
X-RAY DIFFRACTIONr_scbond_it2.2941.5752072
X-RAY DIFFRACTIONr_scbond_other2.2931.5752073
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.382.243011
X-RAY DIFFRACTIONr_long_range_B_refined4.16715.654805
X-RAY DIFFRACTIONr_long_range_B_other4.15915.6174794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 306 -
Rwork0.245 5835 -
obs--97.97 %

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