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Basic information

Entry
Database: PDB / ID: 7wg1
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: 2.19 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 27, 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
B: Arginyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9874
Polymers115,8572
Non-polymers1312
Water7,332407
1
A: Arginyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9942
Polymers57,9281
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arginyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9942
Polymers57,9281
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.088, 107.736, 161.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Arginyltransferase / Arginyl tRNA protein transferase 1


Mass: 57928.262 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 52.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 120mM alcohols (Molecular dimensions), 100mM buffer system 2 pH 7.5 (Molecular dimensions), 37.5% (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: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 62337 / % possible obs: 99.9 % / Redundancy: 5.7 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.072 / Rrim(I) all: 0.174 / Rsym value: 0.158 / Χ2: 0.534 / Net I/σ(I): 8.773
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 1.038 / Num. unique obs: 3042 / CC1/2: 0.649 / CC star: 0.887 / Rpim(I) all: 0.414 / Rrim(I) all: 0.847 / Rsym value: 0.733 / Χ2: 0.437 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.19→48.16 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 2000 3.21 %
Rwork0.1784 --
obs0.1802 62248 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.19→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7933 0 2 407 8342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128125
X-RAY DIFFRACTIONf_angle_d1.11111001
X-RAY DIFFRACTIONf_dihedral_angle_d6.0351069
X-RAY DIFFRACTIONf_chiral_restr0.0571192
X-RAY DIFFRACTIONf_plane_restr0.0091408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.240.33951220.26313689X-RAY DIFFRACTION86
2.24-2.30.3281420.24014258X-RAY DIFFRACTION100
2.3-2.370.29641430.21574281X-RAY DIFFRACTION100
2.37-2.450.26511420.21044302X-RAY DIFFRACTION100
2.45-2.540.30891420.20814284X-RAY DIFFRACTION100
2.54-2.640.26591430.19584303X-RAY DIFFRACTION100
2.64-2.760.25131440.19364341X-RAY DIFFRACTION100
2.76-2.90.26211440.19584315X-RAY DIFFRACTION100
2.9-3.080.25351430.20054332X-RAY DIFFRACTION100
3.08-3.320.23321440.1844340X-RAY DIFFRACTION100
3.32-3.660.2031460.17144382X-RAY DIFFRACTION100
3.66-4.190.20961440.14894372X-RAY DIFFRACTION100
4.19-5.270.17021470.13744430X-RAY DIFFRACTION100
5.27-48.160.22681540.16554619X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.6697 Å / Origin y: 5.5575 Å / Origin z: 14.231 Å
111213212223313233
T0.1912 Å2-0.0115 Å20.0126 Å2-0.1802 Å20.0263 Å2--0.2042 Å2
L0.2086 °2-0.0883 °20.2882 °2-0.035 °20.033 °2--0.611 °2
S0.0602 Å °0.012 Å °-0.0033 Å °-0.0028 Å °0.0087 Å °-0.0109 Å °0.1893 Å °0.0389 Å °0.0017 Å °
Refinement TLS groupSelection details: all

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