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- PDB-4r4y: Structural basis of a point mutation that causes the genetic dise... -

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Basic information

Entry
Database: PDB / ID: 4r4y
TitleStructural basis of a point mutation that causes the genetic disease Aspartylglucosaminuria
ComponentsN(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
KeywordsHYDROLASE / AGU structure / autoprocessing / glycosylasparaginase / lysosomal storage disease / pre-autoproteolysis trap
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
N-hydroxy-L-asparagine / N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
Similarity search - Component
Biological speciesElizabethkingia miricola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSui, L. / Damodharan, L. / Pande, S. / Guo, H.C.
CitationJournal: Structure / Year: 2014
Title: Structural Basis of a Point Mutation that Causes the Genetic Disease Aspartylglucosaminuria.
Authors: Sui, L. / Lakshminarasimhan, D. / Pande, S. / Guo, H.C.
History
DepositionAug 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6233
Polymers64,4752
Non-polymers1481
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-16 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.810, 50.620, 61.230
Angle α, β, γ (deg.)86.28, 91.04, 107.75
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 32237.668 Da / Num. of mol.: 2 / Fragment: UNP residues 46-340 / Mutation: G172D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia miricola (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase
#2: Chemical ChemComp-SD4 / N-hydroxy-L-asparagine


Type: L-peptide linking / Mass: 148.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 0.2M NaCl, 0.1M Bis-Tris pH 6.5, 25% PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111)CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 27448 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.052 / Rsym value: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 9.5 / Rsym value: 0.113 / % possible all: 90.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.864 / SU B: 5.223 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1385 5.1 %RANDOM
Rwork0.19 ---
obs0.194 26039 89.9 %-
all-26039 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20.09 Å20.01 Å2
2--0.11 Å20.07 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 10 87 4413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194385
X-RAY DIFFRACTIONr_bond_other_d0.0010.024263
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9535912
X-RAY DIFFRACTIONr_angle_other_deg0.85839802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7685560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59224.897194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95415780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6491525
X-RAY DIFFRACTIONr_chiral_restr0.1040.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02972
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 95 -
Rwork0.192 1925 -
obs--90.54 %

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