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- PDB-8jjh: Crystal structure of QH-hNTAQ1 C28S -

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Basic information

Entry
Database: PDB / ID: 8jjh
TitleCrystal structure of QH-hNTAQ1 C28S
ComponentsProtein N-terminal glutamine amidohydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


protein N-terminal glutamine amidohydrolase / protein-N-terminal glutamine amidohydrolase activity / protein-N-terminal asparagine amidohydrolase activity / protein modification process / nucleus / cytosol
Similarity search - Function
Protein N-terminal glutamine amidohydrolase, alpha beta roll / Protein N-terminal glutamine amidohydrolase, alpha beta roll superfamily / Protein N-terminal glutamine amidohydrolase / N-terminal glutamine amidase
Similarity search - Domain/homology
Protein N-terminal glutamine amidohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsKang, J.M. / Han, B.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019R1A2C109025 Korea, Republic Of
CitationJournal: Protein Sci. / Year: 2024
Title: Structural study for substrate recognition of human N-terminal glutamine amidohydrolase 1 in the arginine N-degron pathway.
Authors: Kang, J.M. / Park, J.S. / Lee, J.S. / Jang, J.Y. / Han, B.W.
History
DepositionMay 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)23,4821
Polymers23,4821
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.617, 64.494, 45.042
Angle α, β, γ (deg.)90.000, 97.673, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Protein N-terminal glutamine amidohydrolase / Protein NH2-terminal glutamine deamidase / N-terminal Gln amidase / Nt(Q)-amidase / WDYHV motif- ...Protein NH2-terminal glutamine deamidase / N-terminal Gln amidase / Nt(Q)-amidase / WDYHV motif-containing protein 1


Mass: 23482.307 Da / Num. of mol.: 1 / Mutation: C28S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTAQ1, C8orf32, WDYHV1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96HA8, protein N-terminal glutamine amidohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, and 25 % (w/v) Polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 29791 / % possible obs: 99.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 12.52 Å2 / CC1/2: 0.998 / Net I/σ(I): 25.97
Reflection shellResolution: 1.61→1.67 Å / Num. unique obs: 2847 / CC1/2: 0.981

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→40.25 Å / SU ML: 0.1316 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.0497
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1816 1489 5 %
Rwork0.1614 28279 -
obs0.1624 29768 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.36 Å2
Refinement stepCycle: LAST / Resolution: 1.61→40.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 0 268 1909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651732
X-RAY DIFFRACTIONf_angle_d0.88772365
X-RAY DIFFRACTIONf_chiral_restr0.0642239
X-RAY DIFFRACTIONf_plane_restr0.0085311
X-RAY DIFFRACTIONf_dihedral_angle_d17.1993235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.660.18461300.16652469X-RAY DIFFRACTION96.55
1.66-1.720.19081350.16822565X-RAY DIFFRACTION99.93
1.72-1.790.21931360.16862592X-RAY DIFFRACTION99.93
1.79-1.870.20381350.17872563X-RAY DIFFRACTION99.96
1.87-1.970.19631360.16892577X-RAY DIFFRACTION99.93
1.97-2.090.20261340.16582551X-RAY DIFFRACTION99.7
2.09-2.250.20041380.16882606X-RAY DIFFRACTION99.75
2.25-2.480.1931330.17122545X-RAY DIFFRACTION99.48
2.48-2.840.19431360.16822594X-RAY DIFFRACTION99.89
2.84-3.580.1661380.15452598X-RAY DIFFRACTION99.89
3.58-40.250.15041380.14472619X-RAY DIFFRACTION99.28

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