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- PDB-7wg4: DVAA-KlAte1 -

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Basic information

Entry
Database: PDB / ID: 7wg4
TitleDVAA-KlAte1
ComponentsArginyltransferase
KeywordsTRANSFERASE / Arginyl-tRNA protein transferase 1
Function / homology
Function and homology information


arginyltransferase / arginyl-tRNA--protein transferase activity / metal ion binding / cytoplasm
Similarity search - Function
N-end aminoacyl transferase, N-terminal / N-end rule aminoacyl transferase, C-terminal / N-end rule aminoacyl transferase / Arginine-tRNA-protein transferase, N terminus / Arginine-tRNA-protein transferase, C terminus / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.51 Å
AuthorsKim, M.K. / Kim, B.H. / Oh, S.-J. / Song, H.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates.
Authors: Kim, B.H. / Kim, M.K. / Oh, S.J. / Nguyen, K.T. / Kim, J.H. / Varshavsky, A. / Hwang, C.S. / Song, H.K.
History
DepositionDec 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9942
Polymers57,9281
Non-polymers651
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.460, 86.460, 160.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Arginyltransferase / Arginyl tRNA protein transferase 1


Mass: 57928.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Gene: KLLA0_A04862g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CXX6, arginyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 60mM Divalents (Molecular dimensions), 100mM buffer system 2 pH 7.5 (Molecular dimensions), 33% (v/v) precipitant Mix 4 (Molecular dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.51→28.57 Å / Num. obs: 93627 / % possible obs: 97.56 % / Redundancy: 17.7 % / Biso Wilson estimate: 24.27 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.27
Reflection shellResolution: 1.51→1.564 Å / Num. unique obs: 9062 / CC1/2: 0.516

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.51→28.57 Å / SU ML: 0.1737 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9578
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2161 4682 5 %
Rwork0.1851 88943 -
obs0.1866 93625 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.04 Å2
Refinement stepCycle: LAST / Resolution: 1.51→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3971 0 1 304 4276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01694068
X-RAY DIFFRACTIONf_angle_d1.36035510
X-RAY DIFFRACTIONf_chiral_restr0.0813597
X-RAY DIFFRACTIONf_plane_restr0.0137706
X-RAY DIFFRACTIONf_dihedral_angle_d5.8004536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.530.30731500.28642841X-RAY DIFFRACTION95.71
1.53-1.550.29741530.28882909X-RAY DIFFRACTION95.81
1.55-1.560.30231500.27442859X-RAY DIFFRACTION96.13
1.56-1.580.32211510.27652867X-RAY DIFFRACTION96.05
1.58-1.60.29591520.26182879X-RAY DIFFRACTION96.16
1.6-1.630.29561520.26252884X-RAY DIFFRACTION96.32
1.63-1.650.34041510.25732869X-RAY DIFFRACTION96.45
1.65-1.670.2841530.24472917X-RAY DIFFRACTION96.42
1.67-1.70.24711530.22452902X-RAY DIFFRACTION96.71
1.7-1.730.27221530.20952902X-RAY DIFFRACTION96.68
1.73-1.760.26941530.20932920X-RAY DIFFRACTION97
1.76-1.790.27961540.20242914X-RAY DIFFRACTION96.97
1.79-1.820.21771530.19992924X-RAY DIFFRACTION97.16
1.82-1.860.2391550.20252933X-RAY DIFFRACTION97.35
1.86-1.90.23571540.19812936X-RAY DIFFRACTION97.51
1.9-1.950.2411550.22931X-RAY DIFFRACTION97.5
1.95-20.24071560.19922963X-RAY DIFFRACTION97.84
2-2.050.23991560.19432965X-RAY DIFFRACTION97.9
2.05-2.110.22851570.1932982X-RAY DIFFRACTION98.03
2.11-2.180.20351540.1922942X-RAY DIFFRACTION98.16
2.18-2.260.20331570.18072982X-RAY DIFFRACTION98.19
2.26-2.350.18711590.17683015X-RAY DIFFRACTION98.48
2.35-2.450.18371570.1692988X-RAY DIFFRACTION98.62
2.45-2.580.20781590.18273013X-RAY DIFFRACTION98.69
2.58-2.740.22741590.19033030X-RAY DIFFRACTION98.88
2.74-2.950.19131610.1873054X-RAY DIFFRACTION99.04
2.95-3.250.22241610.19123060X-RAY DIFFRACTION98.86
3.25-3.720.2281630.17743103X-RAY DIFFRACTION99.24
3.72-4.680.16971660.1483138X-RAY DIFFRACTION99.61
4.69-28.570.21631750.17723321X-RAY DIFFRACTION99.54

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