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- PDB-6kgj: M1Q-hNTAQ1 C28S -

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Basic information

Entry
Database: PDB / ID: 6kgj
TitleM1Q-hNTAQ1 C28S
ComponentsProtein N-terminal glutamine amidohydrolase
KeywordsHYDROLASE / NTAQ1
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 / Protein N-terminal glutamine amidohydrolase, alpha beta roll superfamily / Protein N-terminal glutamine amidohydrolase / N-terminal glutamine amidase / C8orf32 fold / Roll / Alpha Beta
Similarity search - Domain/homology
Protein N-terminal glutamine amidohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPark, M.R. / Kim, L. / Kwon, D.H. / Song, H.K.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Use of the LC3B-fusion technique for biochemical and structural studies of proteins involved in the N-degron pathway.
Authors: Kim, L. / Kwon, D.H. / Heo, J. / Park, M.R. / Song, H.K.
History
DepositionJul 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)46,4262
Polymers46,4262
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-6 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.638, 105.779, 140.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 23212.963 Da / Num. of mol.: 2 / Mutation: C28S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDYHV1, C8orf32, NTAQ1 / 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: 3.82 Å3/Da / Density % sol: 67.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.4M ammonium sulfate, 0.1M sodium citrate tribasic dihydrate pH 5.6, 1.0M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 65207 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 25.9
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 6176

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W79

4w79


Resolution: 1.8→35.47 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / Phase error: 22.12
RfactorNum. reflection% reflection
Rfree0.223 2000 3.07 %
Rwork0.2111 --
obs0.2115 65207 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.83 Å2 / Biso mean: 26.6971 Å2 / Biso min: 14.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 0 156 3426
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8044-1.84960.29171330.23894196432994
1.8496-1.89960.26451410.226744674608100
1.8996-1.95540.2571440.225445354679100
1.9554-2.01860.2561400.220244474587100
2.0186-2.09070.27081440.219845234667100
2.0907-2.17440.24051420.212844904632100
2.1744-2.27330.23861430.212745244667100
2.2733-2.39320.23591420.215844964638100
2.3932-2.54310.23251420.233545104652100
2.5431-2.73940.25771450.2445394684100
2.7394-3.01490.25551430.234845444687100
3.0149-3.45080.21851440.223645714715100
3.4508-4.34650.19231470.183546034750100
4.3465-35.47750.17471500.182747574907100

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