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- PDB-8jjf: Crystal structure of QE-hNTAQ1 C28S -

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Basic information

Entry
Database: PDB / ID: 8jjf
TitleCrystal structure of QE-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: 1.51 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
A: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)23,4731
Polymers23,4731
Non-polymers00
Water5,423301
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)40.611, 64.337, 45.140
Angle α, β, γ (deg.)90.000, 97.880, 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: 23473.273 Da / Num. of mol.: 1 / Mutation: G-2Q, H-1E, C28S
Source method: isolated from a genetically manipulated source
Details: The first two amino acids from the sequence (QE) are positioned -2 and -1, respectively. The sequence should start from MEGPAA-.
Source: (gene. exp.) Homo sapiens (human) / Gene: NTAQ1, C8orf32, WDYHV1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q96HA8, protein N-terminal glutamine amidohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 50.57 %
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 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 36172 / % possible obs: 99.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 13.68 Å2 / CC1/2: 0.994 / Net I/σ(I): 15.96
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 4.2 % / Num. unique obs: 1744 / CC1/2: 0.574 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→34.11 Å / SU ML: 0.1273 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1899 1641 5 %
Rwork0.1728 31178 -
obs0.1737 32819 90.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.9 Å2
Refinement stepCycle: LAST / Resolution: 1.51→34.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 0 301 1941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451715
X-RAY DIFFRACTIONf_angle_d0.75912340
X-RAY DIFFRACTIONf_chiral_restr0.0555238
X-RAY DIFFRACTIONf_plane_restr0.0064307
X-RAY DIFFRACTIONf_dihedral_angle_d21.2033230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.550.2434940.21411808X-RAY DIFFRACTION63.15
1.55-1.60.22731090.20052070X-RAY DIFFRACTION72.8
1.6-1.660.22041210.19772299X-RAY DIFFRACTION80.21
1.66-1.730.23011320.19722489X-RAY DIFFRACTION86.82
1.73-1.80.23791370.19592620X-RAY DIFFRACTION91.59
1.8-1.90.20551450.19452749X-RAY DIFFRACTION95.7
1.9-2.020.23631450.18462748X-RAY DIFFRACTION96.27
2.02-2.170.19441510.17592876X-RAY DIFFRACTION99.44
2.17-2.390.19211510.17892869X-RAY DIFFRACTION99.83
2.39-2.740.2161500.18112843X-RAY DIFFRACTION99.63
2.74-3.450.17361520.16572894X-RAY DIFFRACTION99.41
3.45-34.110.14681540.14452913X-RAY DIFFRACTION99.35

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