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- PDB-7wg2: EVAA-KlAte1 -

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Basic information

Entry
Database: PDB / ID: 7wg2
TitleEVAA-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: 1.76 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)58,0082
Polymers57,9421
Non-polymers651
Water6,107339
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)86.600, 86.600, 161.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw

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Components

#1: Protein Arginyltransferase / Arginyl tRNA protein transferase 1


Mass: 57942.285 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: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
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: 1.76→29.49 Å / Num. obs: 61443 / % possible obs: 99.93 % / Redundancy: 26.5 % / Biso Wilson estimate: 25.87 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.99
Reflection shellResolution: 1.76→1.823 Å / Num. unique obs: 6037 / CC1/2: 0.711

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.76→29.49 Å / SU ML: 0.2186 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5507
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2121 3073 5 %
Rwork0.1795 58360 -
obs0.1812 61433 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.2 Å2
Refinement stepCycle: LAST / Resolution: 1.76→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3948 0 1 339 4288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01054043
X-RAY DIFFRACTIONf_angle_d1.07295473
X-RAY DIFFRACTIONf_chiral_restr0.0612593
X-RAY DIFFRACTIONf_plane_restr0.0111700
X-RAY DIFFRACTIONf_dihedral_angle_d5.9114531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.790.35571370.34682599X-RAY DIFFRACTION99.89
1.79-1.820.30481370.28552590X-RAY DIFFRACTION99.96
1.82-1.850.31561390.26872641X-RAY DIFFRACTION99.96
1.85-1.880.27381370.2522607X-RAY DIFFRACTION99.89
1.88-1.920.27671370.21632608X-RAY DIFFRACTION100
1.92-1.960.21581370.19882601X-RAY DIFFRACTION99.96
1.96-20.2271370.19192610X-RAY DIFFRACTION99.96
2-2.050.23771390.18862631X-RAY DIFFRACTION99.96
2.05-2.10.22821370.1962606X-RAY DIFFRACTION100
2.1-2.150.21041400.19072650X-RAY DIFFRACTION99.93
2.15-2.220.20571370.16182605X-RAY DIFFRACTION100
2.22-2.290.20061390.15562643X-RAY DIFFRACTION99.93
2.29-2.370.19341380.15862631X-RAY DIFFRACTION100
2.37-2.470.19511400.15972657X-RAY DIFFRACTION99.96
2.47-2.580.20441380.16382626X-RAY DIFFRACTION100
2.58-2.710.20021410.17672679X-RAY DIFFRACTION100
2.71-2.880.21311400.17982654X-RAY DIFFRACTION100
2.88-3.110.21271410.18412677X-RAY DIFFRACTION100
3.11-3.420.22761410.18352680X-RAY DIFFRACTION100
3.42-3.910.21011430.16872713X-RAY DIFFRACTION100
3.91-4.920.16631440.14592747X-RAY DIFFRACTION100
4.93-29.490.21681540.18962905X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 26.3073367442 Å / Origin y: -6.84595739382 Å / Origin z: 13.2674168783 Å
111213212223313233
T0.133741755234 Å20.0144746762745 Å20.0148458318796 Å2-0.181240427196 Å2-0.0102130579828 Å2--0.144212370015 Å2
L1.21737250546 °20.214428238975 °20.00511863442937 °2-0.581597914827 °2-0.157278045146 °2--0.718275094886 °2
S-0.0142612880936 Å °-0.172758226713 Å °0.0406545180113 Å °-0.00256990979824 Å °-0.016429783195 Å °-0.0183314958013 Å °-0.0382336272481 Å °0.0859921139234 Å °-0.000508639612633 Å °
Refinement TLS groupSelection details: all

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