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- PDB-8jjy: Crystal structure of QN-hNTAQ1 C28S -

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Basic information

Entry
Database: PDB / ID: 8jjy
TitleCrystal structure of QN-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: 1.69 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)46,9172
Polymers46,9172
Non-polymers00
Water7,494416
1
A: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)23,4581
Polymers23,4581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)23,4581
Polymers23,4581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.990, 64.500, 80.131
Angle α, β, γ (deg.)90.000, 98.950, 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: 23458.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gln-2 and Asn-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.: 416 / 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: 2.39 Å3/Da / Density % sol: 48.61 %
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: 1.69→50 Å / Num. obs: 48685 / % possible obs: 99 % / Redundancy: 4.9 % / Biso Wilson estimate: 14.18 Å2 / CC1/2: 0.986 / Net I/σ(I): 12.04
Reflection shellResolution: 1.69→1.73 Å / Num. unique obs: 2335 / CC1/2: 0.699

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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: 1.69→43.45 Å / SU ML: 0.1599 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.6798
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1886 2118 5 %
Rwork0.1666 40227 -
obs0.1677 42345 85.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.4 Å2
Refinement stepCycle: LAST / Resolution: 1.69→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 0 416 3698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773433
X-RAY DIFFRACTIONf_angle_d0.94224688
X-RAY DIFFRACTIONf_chiral_restr0.0677476
X-RAY DIFFRACTIONf_plane_restr0.0087618
X-RAY DIFFRACTIONf_dihedral_angle_d19.1873463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.730.258780.19441479X-RAY DIFFRACTION47.79
1.73-1.780.2579980.19091867X-RAY DIFFRACTION59.95
1.78-1.820.21841050.18092002X-RAY DIFFRACTION64.69
1.82-1.880.23721160.19142175X-RAY DIFFRACTION70.21
1.88-1.940.26261250.19552394X-RAY DIFFRACTION76.19
1.94-2.010.22841360.18182591X-RAY DIFFRACTION83.24
2.01-2.090.20781520.1792868X-RAY DIFFRACTION92.35
2.09-2.180.20661610.17133076X-RAY DIFFRACTION97.68
2.18-2.30.22451620.16753067X-RAY DIFFRACTION98.69
2.3-2.440.18691620.17753079X-RAY DIFFRACTION98.39
2.44-2.630.19291610.18123049X-RAY DIFFRACTION98.59
2.63-2.890.21791640.17463128X-RAY DIFFRACTION99.04
2.9-3.310.1621640.16223106X-RAY DIFFRACTION99
3.31-4.170.16291640.13933123X-RAY DIFFRACTION99.43
4.17-43.450.14121700.1533223X-RAY DIFFRACTION99.62
Refinement TLS params.Method: refined / Origin x: 14.8804280428 Å / Origin y: 13.1641228534 Å / Origin z: -13.6675219396 Å
111213212223313233
T0.0775671935963 Å20.00471599836896 Å2-0.0093648457483 Å2-0.0650617549265 Å20.00546218011256 Å2--0.103210012423 Å2
L0.182971646436 °20.0497668996039 °2-0.186182815088 °2-0.176266622304 °2-0.0245322205853 °2--1.29777944458 °2
S-0.00201394902145 Å °-0.0125578917698 Å °-0.000641330267933 Å °0.00601446639775 Å °0.00279478163837 Å °0.00668816022065 Å °0.0302905299853 Å °-0.0222211761708 Å °-0.00103089959333 Å °
Refinement TLS groupSelection details: all

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