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- PDB-8jk2: Crystal structure of QF-hNTAQ1 C28S -

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Basic information

Entry
Database: PDB / ID: 8jk2
TitleCrystal structure of QF-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: 1.742 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
B: Protein N-terminal glutamine amidohydrolase
A: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)46,9832
Polymers46,9832
Non-polymers00
Water5,206289
1
B: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)23,4911
Polymers23,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)23,4911
Polymers23,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.707, 64.128, 79.989
Angle α, β, γ (deg.)90.000, 98.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein N-terminal glutamine amidohydrolase


Mass: 23491.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gln-2 and Phe-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.: 289 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
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: Apr 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 41778 / % possible obs: 93.4 % / Redundancy: 5.8 % / CC1/2: 0.991 / Net I/σ(I): 11.52
Reflection shellResolution: 1.74→1.78 Å / Num. unique obs: 1790 / CC1/2: 0.823

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
d*TREKdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.742→35.861 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.79 / SU ML: 0.09 / Cross valid method: FREE R-VALUE / ESU R: 0.187 / ESU R Free: 0.16
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2364 1617 4.999 %
Rwork0.2015 30732 -
all0.203 --
obs-32349 72.18 %
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: 22.673 Å2
Baniso -1Baniso -2Baniso -3
1-1.669 Å2-0 Å2-0.025 Å2
2---0.774 Å20 Å2
3----0.848 Å2
Refinement stepCycle: LAST / Resolution: 1.742→35.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 0 289 3573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133429
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153018
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.6474675
X-RAY DIFFRACTIONr_angle_other_deg1.1751.5797015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0265414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.85622.526190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2215533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7371518
X-RAY DIFFRACTIONr_chiral_restr0.0530.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023916
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
X-RAY DIFFRACTIONr_nbd_refined0.2010.2583
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.22704
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21610
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.21466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2254
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1470.228
X-RAY DIFFRACTIONr_nbd_other0.1810.2141
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.219
X-RAY DIFFRACTIONr_mcbond_it1.3532.3491629
X-RAY DIFFRACTIONr_mcbond_other1.3472.3471628
X-RAY DIFFRACTIONr_mcangle_it2.3693.5082034
X-RAY DIFFRACTIONr_mcangle_other2.3693.5092035
X-RAY DIFFRACTIONr_scbond_it1.4072.4061800
X-RAY DIFFRACTIONr_scbond_other1.4072.4051799
X-RAY DIFFRACTIONr_scangle_it2.2973.5532635
X-RAY DIFFRACTIONr_scangle_other2.2953.5522635
X-RAY DIFFRACTIONr_lrange_it4.53326.5453871
X-RAY DIFFRACTIONr_lrange_other4.29326.1133808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.742-1.7870.241600.2271139X-RAY DIFFRACTION36.4881
1.787-1.8360.255730.2011367X-RAY DIFFRACTION44.7761
1.836-1.8890.218750.1951479X-RAY DIFFRACTION49.5062
1.889-1.9470.239780.2091567X-RAY DIFFRACTION54.7603
1.947-2.0110.239870.211691X-RAY DIFFRACTION60.2712
2.011-2.0820.2951070.2091775X-RAY DIFFRACTION65.7123
2.082-2.160.267900.2121866X-RAY DIFFRACTION71.9118
2.16-2.2480.2311070.2091831X-RAY DIFFRACTION73.8005
2.248-2.3480.2611120.1991958X-RAY DIFFRACTION80.5447
2.348-2.4620.2331040.1961912X-RAY DIFFRACTION83.4783
2.462-2.5950.24870.2112122X-RAY DIFFRACTION94.2808
2.595-2.7520.2261070.2052049X-RAY DIFFRACTION98.5375
2.752-2.9410.2211060.191896X-RAY DIFFRACTION97.7539
2.941-3.1760.22990.1881751X-RAY DIFFRACTION96.9094
3.176-3.4780.213780.1821596X-RAY DIFFRACTION94.0978
3.478-3.8860.203540.1821398X-RAY DIFFRACTION90.411
3.886-4.4820.229670.1911088X-RAY DIFFRACTION80.8824
4.482-5.4790.209560.192934X-RAY DIFFRACTION81.2808
5.479-7.7020.271540.243808X-RAY DIFFRACTION91.5074
7.702-35.8610.388160.267505X-RAY DIFFRACTION94.3841

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