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- PDB-8jjw: Crystal structure of QG-hNTAQ1 C28S -

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Basic information

Entry
Database: PDB / ID: 8jjw
TitleCrystal structure of QG-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: 1.4 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8755
Polymers46,8022
Non-polymers733
Water8,431468
1
A: Protein N-terminal glutamine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4262
Polymers23,4011
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10890 Å2
MethodPISA
2
B: Protein N-terminal glutamine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4503
Polymers23,4011
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area10610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.084, 64.688, 80.262
Angle α, β, γ (deg.)90.000, 98.821, 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: 23401.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gln-2 and Gly-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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.1 %
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: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 84546 / % possible obs: 96.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 13.07 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.58
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 4219 / CC1/2: 0.869

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→43.56 Å / SU ML: 0.1239 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.6934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1893 4140 5 %
Rwork0.1736 78656 -
obs0.1744 82796 94.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.34 Å2
Refinement stepCycle: LAST / Resolution: 1.4→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 3 468 3745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00553438
X-RAY DIFFRACTIONf_angle_d0.80464695
X-RAY DIFFRACTIONf_chiral_restr0.086476
X-RAY DIFFRACTIONf_plane_restr0.0063618
X-RAY DIFFRACTIONf_dihedral_angle_d17.5346467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.24071100.21682089X-RAY DIFFRACTION76.06
1.42-1.430.2511210.22322304X-RAY DIFFRACTION83.13
1.43-1.450.22131280.20832433X-RAY DIFFRACTION88.28
1.45-1.470.27251290.21192446X-RAY DIFFRACTION88.67
1.47-1.490.25821340.20192548X-RAY DIFFRACTION93.87
1.49-1.510.2251380.19512611X-RAY DIFFRACTION94.02
1.51-1.530.22881400.19982651X-RAY DIFFRACTION95.84
1.53-1.550.23221370.18822613X-RAY DIFFRACTION95.25
1.55-1.580.19351310.18722511X-RAY DIFFRACTION90.2
1.58-1.60.2271390.18662630X-RAY DIFFRACTION96.31
1.6-1.630.20551440.18392731X-RAY DIFFRACTION97.06
1.63-1.660.18851380.17872626X-RAY DIFFRACTION97.08
1.66-1.690.19381420.17982693X-RAY DIFFRACTION96.43
1.69-1.730.20961380.17032634X-RAY DIFFRACTION96.25
1.73-1.770.17391410.16972669X-RAY DIFFRACTION96.86
1.77-1.810.20171430.1762714X-RAY DIFFRACTION98.35
1.81-1.850.18441430.17322719X-RAY DIFFRACTION98.01
1.85-1.90.18191420.17512703X-RAY DIFFRACTION97.6
1.9-1.960.17151380.1712620X-RAY DIFFRACTION94.65
1.96-2.020.21471390.18022640X-RAY DIFFRACTION94.91
2.02-2.090.19461410.17732675X-RAY DIFFRACTION97.41
2.09-2.180.18391430.16852712X-RAY DIFFRACTION97.77
2.18-2.280.20521420.1722713X-RAY DIFFRACTION97.67
2.28-2.40.1891420.17882694X-RAY DIFFRACTION97.06
2.4-2.550.18881430.18182706X-RAY DIFFRACTION97.67
2.55-2.740.20561400.18432665X-RAY DIFFRACTION96.26
2.74-3.020.16431380.17842606X-RAY DIFFRACTION93.78
3.02-3.460.17711460.16442788X-RAY DIFFRACTION99.19
3.46-4.350.14031460.14552775X-RAY DIFFRACTION98.95
4.35-43.560.21440.16332737X-RAY DIFFRACTION95.62

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