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- PDB-8jk1: Crystal structure of QA-hNTAQ1 C28S -

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Basic information

Entry
Database: PDB / ID: 8jk1
TitleCrystal structure of QA-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: 2.067 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)46,8302
Polymers46,8302
Non-polymers00
Water3,333185
1
A: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)23,4151
Polymers23,4151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)23,4151
Polymers23,4151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.059, 64.125, 80.042
Angle α, β, γ (deg.)90.000, 98.873, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein N-terminal glutamine amidohydrolase


Mass: 23415.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.: 185 / 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: 48.44 %
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: 2.05→50 Å / Num. obs: 25723 / % possible obs: 95.2 % / Redundancy: 5.3 % / CC1/2: 0.995 / Net I/σ(I): 15.87
Reflection shellResolution: 2.05→2.09 Å / Num. unique obs: 1276 / CC1/2: 0.744

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
d*TREKdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.067→43.57 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.967 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / ESU R: 0.293 / ESU R Free: 0.193
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2194 1145 4.922 %
Rwork0.2036 22120 -
all0.204 --
obs-23265 85.703 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.274 Å2
Baniso -1Baniso -2Baniso -3
1-1.216 Å2-0 Å20.055 Å2
2---0.668 Å20 Å2
3----0.539 Å2
Refinement stepCycle: LAST / Resolution: 2.067→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 0 185 3465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133404
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153005
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.6464637
X-RAY DIFFRACTIONr_angle_other_deg1.0841.5816977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4845408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.1322.553188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91615527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8641518
X-RAY DIFFRACTIONr_chiral_restr0.0410.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023883
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02801
X-RAY DIFFRACTIONr_nbd_refined0.1810.2573
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.22622
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21605
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.21465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2150
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1590.229
X-RAY DIFFRACTIONr_nbd_other0.1950.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.29
X-RAY DIFFRACTIONr_mcbond_it1.273.0351626
X-RAY DIFFRACTIONr_mcbond_other1.2693.0341625
X-RAY DIFFRACTIONr_mcangle_it2.3324.542027
X-RAY DIFFRACTIONr_mcangle_other2.3324.5412028
X-RAY DIFFRACTIONr_scbond_it0.9322.9911778
X-RAY DIFFRACTIONr_scbond_other0.932.991777
X-RAY DIFFRACTIONr_scangle_it1.6674.4572607
X-RAY DIFFRACTIONr_scangle_other1.6674.4572607
X-RAY DIFFRACTIONr_lrange_it4.28833.4533734
X-RAY DIFFRACTIONr_lrange_other4.17133.3073710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.067-2.1210.262600.2371152X-RAY DIFFRACTION60.7823
2.121-2.1790.265650.2441225X-RAY DIFFRACTION66.2898
2.179-2.2420.278650.231281X-RAY DIFFRACTION71.672
2.242-2.3110.286720.2351297X-RAY DIFFRACTION74.2005
2.311-2.3860.26590.2261348X-RAY DIFFRACTION79.8978
2.386-2.470.277700.221362X-RAY DIFFRACTION82.6313
2.47-2.5630.22700.2171410X-RAY DIFFRACTION88.2002
2.563-2.6670.264680.2271390X-RAY DIFFRACTION91.182
2.667-2.7850.227660.2221322X-RAY DIFFRACTION90.719
2.785-2.9210.23750.2031313X-RAY DIFFRACTION94.2935
2.921-3.0780.197600.1931253X-RAY DIFFRACTION94.8014
3.078-3.2640.187620.1871204X-RAY DIFFRACTION95.2596
3.264-3.4890.213600.1711138X-RAY DIFFRACTION96.3023
3.489-3.7670.189580.1731117X-RAY DIFFRACTION99.2399
3.767-4.1240.218680.178988X-RAY DIFFRACTION99.5287
4.124-4.6070.163510.181916X-RAY DIFFRACTION99.1795
4.607-5.3120.185340.189831X-RAY DIFFRACTION99.7693
5.312-6.4870.264370.241705X-RAY DIFFRACTION100
6.487-9.0980.18210.23556X-RAY DIFFRACTION100
9.098-43.570.255240.241312X-RAY DIFFRACTION99.115

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