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- PDB-8jk0: Crystal structure of QL-hNTAQ1 C28S -

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Basic information

Entry
Database: PDB / ID: 8jk0
TitleCrystal structure of QL-hNTAQ1 C28S
ComponentsProtein N-terminal glutamine amidohydrolase
KeywordsHYDROLASE
Function / homology:
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 31, 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)23,4571
Polymers23,4571
Non-polymers00
Water4,810267
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)40.545, 64.502, 45.053
Angle α, β, γ (deg.)90.000, 98.180, 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


Mass: 23457.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gln-2 and Leu-1 are added to the N-terminus. / Source: (gene. exp.) Homo sapiens (human) / Gene: C8orf32 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A024R9I8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 50.52 %
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: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 40425 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 14.17 Å2 / CC1/2: 0.995 / Net I/σ(I): 17.02
Reflection shellResolution: 1.45→1.48 Å / Num. unique obs: 1992 / CC1/2: 0.734

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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: 1.45→44.59 Å / SU ML: 0.1589 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.0855
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1968 1937 5 %
Rwork0.17 36832 -
obs0.1713 38769 95.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.76 Å2
Refinement stepCycle: LAST / Resolution: 1.45→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 0 267 1910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581718
X-RAY DIFFRACTIONf_angle_d0.85642345
X-RAY DIFFRACTIONf_chiral_restr0.088239
X-RAY DIFFRACTIONf_plane_restr0.0089308
X-RAY DIFFRACTIONf_dihedral_angle_d20.8257231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.3209940.2741809X-RAY DIFFRACTION66.61
1.49-1.530.2871200.23552267X-RAY DIFFRACTION82.48
1.53-1.570.22491370.20022600X-RAY DIFFRACTION95.23
1.57-1.630.23041430.20252714X-RAY DIFFRACTION98.79
1.63-1.680.23821420.19682700X-RAY DIFFRACTION99.34
1.68-1.750.22891450.19452750X-RAY DIFFRACTION99.66
1.75-1.830.23561420.20132728X-RAY DIFFRACTION99.76
1.83-1.930.21091430.17232729X-RAY DIFFRACTION99.65
1.93-2.050.1891440.16892730X-RAY DIFFRACTION99.62
2.05-2.210.1891430.16592721X-RAY DIFFRACTION99.79
2.21-2.430.17141440.16792747X-RAY DIFFRACTION99.86
2.43-2.780.20641460.17092764X-RAY DIFFRACTION99.9
2.78-3.50.18621460.162767X-RAY DIFFRACTION99.97
3.5-44.590.16981480.14292806X-RAY DIFFRACTION99.73

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