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- PDB-8jji: Crystal structure of QR-hNTAQ1 C28S -

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Basic information

Entry
Database: PDB / ID: 8jji
TitleCrystal structure of QR-hNTAQ1 C28S
ComponentsProtein N-terminal glutamine amidohydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


protein N-terminal glutamine amidohydrolase / protein-N-terminal glutamine amidohydrolase activity / protein-N-terminal asparagine amidohydrolase activity / protein modification process / nucleus / cytosol
Similarity search - Function
Protein N-terminal glutamine amidohydrolase, alpha beta roll / Protein N-terminal glutamine amidohydrolase, alpha beta roll superfamily / Protein N-terminal glutamine amidohydrolase / N-terminal glutamine amidase
Similarity search - Domain/homology
Protein N-terminal glutamine amidohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.206 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 30, 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
B: Protein N-terminal glutamine amidohydrolase
A: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)47,0032
Polymers47,0032
Non-polymers00
Water2,810156
1
B: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)23,5011
Polymers23,5011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)23,5011
Polymers23,5011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.621, 64.781, 80.617
Angle α, β, γ (deg.)90.000, 98.361, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein N-terminal glutamine amidohydrolase / Protein NH2-terminal glutamine deamidase / N-terminal Gln amidase / Nt(Q)-amidase / WDYHV motif- ...Protein NH2-terminal glutamine deamidase / N-terminal Gln amidase / Nt(Q)-amidase / WDYHV motif-containing protein 1


Mass: 23501.354 Da / Num. of mol.: 2 / Mutation: Q-1, R0, C28S
Source method: isolated from a genetically manipulated source
Details: Gln-1 and Arg0 are added to the N-terminus. / Source: (gene. exp.) Homo sapiens (human) / Gene: NTAQ1, C8orf32, WDYHV1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96HA8, protein N-terminal glutamine amidohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
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: Nov 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 22882 / % possible obs: 99.7 % / Redundancy: 4 % / CC1/2: 0.977 / Net I/σ(I): 12.78
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 1144 / CC1/2: 0.841

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
d*TREKdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.206→44.186 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.72 / SU ML: 0.145 / Cross valid method: FREE R-VALUE / ESU R: 0.327 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2286 1091 5.008 %
Rwork0.2021 20695 -
all0.203 --
obs-21786 94.422 %
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: 29.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.619 Å20 Å20.261 Å2
2---0.591 Å2-0 Å2
3----0.101 Å2
Refinement stepCycle: LAST / Resolution: 2.206→44.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 0 156 3448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133400
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152998
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.6484624
X-RAY DIFFRACTIONr_angle_other_deg1.071.5826954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.97222.292192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06315528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9491520
X-RAY DIFFRACTIONr_chiral_restr0.040.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02808
X-RAY DIFFRACTIONr_nbd_refined0.1770.2518
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.22547
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21587
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.21409
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2146
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1140.219
X-RAY DIFFRACTIONr_nbd_other0.150.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.212
X-RAY DIFFRACTIONr_mcbond_it1.2633.1781620
X-RAY DIFFRACTIONr_mcbond_other1.2623.1771619
X-RAY DIFFRACTIONr_mcangle_it2.2754.7512018
X-RAY DIFFRACTIONr_mcangle_other2.2754.7522019
X-RAY DIFFRACTIONr_scbond_it1.1073.1931780
X-RAY DIFFRACTIONr_scbond_other1.1063.1921779
X-RAY DIFFRACTIONr_scangle_it1.9514.7442606
X-RAY DIFFRACTIONr_scangle_other1.954.7442606
X-RAY DIFFRACTIONr_lrange_it3.7834.3833661
X-RAY DIFFRACTIONr_lrange_other3.69434.2763639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.206-2.2630.274660.2371243X-RAY DIFFRACTION78.1026
2.263-2.3250.251690.221331X-RAY DIFFRACTION84.2866
2.325-2.3920.266640.2281325X-RAY DIFFRACTION85.8467
2.392-2.4660.252660.2221320X-RAY DIFFRACTION89.0173
2.466-2.5470.254630.2121328X-RAY DIFFRACTION92.9813
2.547-2.6360.292700.2181330X-RAY DIFFRACTION94.2761
2.636-2.7350.205570.2121318X-RAY DIFFRACTION99.0634
2.735-2.8460.255750.2081284X-RAY DIFFRACTION99.7065
2.846-2.9720.23770.2071242X-RAY DIFFRACTION99.8486
2.972-3.1170.222560.191183X-RAY DIFFRACTION99.8388
3.117-3.2850.198460.181139X-RAY DIFFRACTION99.8315
3.285-3.4830.208630.1881061X-RAY DIFFRACTION99.6454
3.483-3.7220.223630.1841001X-RAY DIFFRACTION99.4393
3.722-4.0190.228540.182930X-RAY DIFFRACTION99.7972
4.019-4.3990.188520.176853X-RAY DIFFRACTION100
4.399-4.9140.143350.174798X-RAY DIFFRACTION98.9311
4.914-5.6650.196330.209691X-RAY DIFFRACTION99.7245
5.665-6.9160.269380.25588X-RAY DIFFRACTION99.6815
6.916-9.6890.225220.225468X-RAY DIFFRACTION99.3915
9.689-44.1860.31220.281262X-RAY DIFFRACTION96.9283

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