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- PDB-8jju: Crystal structure of QD-hNTAQ1 C28S -

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Basic information

Entry
Database: PDB / ID: 8jju
TitleCrystal structure of QD-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: 1.46 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
B: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)46,9182
Polymers46,9182
Non-polymers00
Water7,927440
1
A: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)23,4591
Polymers23,4591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)23,4591
Polymers23,4591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.896, 64.373, 80.047
Angle α, β, γ (deg.)90.000, 99.070, 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: 23459.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gln-2 and Asp-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.: 440 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
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: 1.46→50 Å / Num. obs: 75385 / % possible obs: 98.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 13.7 Å2 / CC1/2: 0.991 / Net I/σ(I): 11.59
Reflection shellResolution: 1.46→1.49 Å / Num. unique obs: 3712 / CC1/2: 0.691

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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: 1.46→35.71 Å / SU ML: 0.1516 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.7333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2043 3308 5 %
Rwork0.1792 62826 -
obs0.1804 66134 86.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.48 Å2
Refinement stepCycle: LAST / Resolution: 1.46→35.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 0 440 3718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01083434
X-RAY DIFFRACTIONf_angle_d1.1354684
X-RAY DIFFRACTIONf_chiral_restr0.1057471
X-RAY DIFFRACTIONf_plane_restr0.0117620
X-RAY DIFFRACTIONf_dihedral_angle_d17.2129456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.480.2969690.20591308X-RAY DIFFRACTION43.69
1.48-1.50.217790.21221502X-RAY DIFFRACTION49.97
1.5-1.530.2701880.20281670X-RAY DIFFRACTION55.06
1.53-1.550.2617970.20211842X-RAY DIFFRACTION61.46
1.55-1.580.23531060.20142018X-RAY DIFFRACTION66.54
1.58-1.610.22591140.19982171X-RAY DIFFRACTION72.04
1.61-1.640.26351240.19932332X-RAY DIFFRACTION78.04
1.64-1.670.28111310.20462488X-RAY DIFFRACTION82.36
1.67-1.710.23281410.20412685X-RAY DIFFRACTION89.29
1.71-1.750.21721530.19022910X-RAY DIFFRACTION96.5
1.75-1.790.23861550.18352931X-RAY DIFFRACTION97.29
1.79-1.840.23231570.17722990X-RAY DIFFRACTION98.47
1.84-1.890.21141560.17612966X-RAY DIFFRACTION98.33
1.89-1.950.19511580.17612987X-RAY DIFFRACTION98.87
1.95-2.020.23241570.17692985X-RAY DIFFRACTION98.59
2.02-2.110.18281570.17563003X-RAY DIFFRACTION98.97
2.11-2.20.19541580.17172989X-RAY DIFFRACTION98.99
2.2-2.320.18561570.17182990X-RAY DIFFRACTION98.56
2.32-2.460.21751570.18242979X-RAY DIFFRACTION98.62
2.46-2.650.21261560.1882970X-RAY DIFFRACTION98.06
2.65-2.920.21261580.18163005X-RAY DIFFRACTION97.87
2.92-3.340.18261590.17583000X-RAY DIFFRACTION98.9
3.34-4.210.18371590.15953028X-RAY DIFFRACTION99.28
4.21-35.710.18051620.18173077X-RAY DIFFRACTION98.36

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