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- PDB-8j6v: Structure of yeast Arginyl-tRNA-protein transferase 1 -

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Basic information

Entry
Database: PDB / ID: 8j6v
TitleStructure of yeast Arginyl-tRNA-protein transferase 1
Componentsarginyltransferase
KeywordsTRANSFERASE / Arginyltransferase
Function / homologyarginyltransferase / arginyl-tRNA--protein transferase activity / 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 / arginyltransferase
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsYashiro, Y. / Tomita, K.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)LS136 Japan
Japan Society for the Promotion of Science (JSPS)18H03980 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)26113002 Japan
Japan Society for the Promotion of Science (JSPS)19K16069 Japan
Japan Society for the Promotion of Science (JSPS)23H00368 Japan
Japan Society for the Promotion of Science (JSPS)22K15055 Japan
CitationJournal: To Be Published
Title: Structure of Arginyl-tRNA-protein transferase 1
Authors: Yashiro, Y. / Tomita, T.
History
DepositionApr 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: arginyltransferase
B: arginyltransferase
D: arginyltransferase
F: arginyltransferase
E: arginyltransferase
L: arginyltransferase
H: arginyltransferase
G: arginyltransferase
C: arginyltransferase
K: arginyltransferase
I: arginyltransferase
J: arginyltransferase


Theoretical massNumber of molelcules
Total (without water)708,87212
Polymers708,87212
Non-polymers00
Water0
1
A: arginyltransferase


Theoretical massNumber of molelcules
Total (without water)59,0731
Polymers59,0731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: arginyltransferase


Theoretical massNumber of molelcules
Total (without water)59,0731
Polymers59,0731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: arginyltransferase


Theoretical massNumber of molelcules
Total (without water)59,0731
Polymers59,0731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: arginyltransferase


Theoretical massNumber of molelcules
Total (without water)59,0731
Polymers59,0731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: arginyltransferase


Theoretical massNumber of molelcules
Total (without water)59,0731
Polymers59,0731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
L: arginyltransferase


Theoretical massNumber of molelcules
Total (without water)59,0731
Polymers59,0731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
H: arginyltransferase


Theoretical massNumber of molelcules
Total (without water)59,0731
Polymers59,0731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
G: arginyltransferase


Theoretical massNumber of molelcules
Total (without water)59,0731
Polymers59,0731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
C: arginyltransferase


Theoretical massNumber of molelcules
Total (without water)59,0731
Polymers59,0731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
K: arginyltransferase


Theoretical massNumber of molelcules
Total (without water)59,0731
Polymers59,0731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
I: arginyltransferase


Theoretical massNumber of molelcules
Total (without water)59,0731
Polymers59,0731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
J: arginyltransferase


Theoretical massNumber of molelcules
Total (without water)59,0731
Polymers59,0731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)235.660, 235.660, 171.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
arginyltransferase /


Mass: 59072.641 Da / Num. of mol.: 12 / Mutation: E339K, E340K, E341K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8H4C2T6

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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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5 M ammonium sulfate, 3 % isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.4→48.57 Å / Num. obs: 128824 / % possible obs: 99.8 % / Redundancy: 13.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.371 / Rrim(I) all: 0.386 / Net I/σ(I): 9.41
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.4-3.492.30594780.5212.3971
3.49-3.581.64792880.6781.7121
3.58-3.691.33489620.7811.3891
3.69-3.81.10487610.8491.1471
3.8-3.920.91984050.8910.9541
3.92-4.060.72282090.930.7481
4.06-4.220.55379330.9570.5731
4.22-4.390.42476370.9730.441
4.39-4.580.31473150.9840.3261
4.58-4.810.29769900.9850.3081
4.81-5.070.28566810.9850.2961
5.07-5.370.28563080.9840.2971
5.37-5.740.2759210.9860.2811
5.74-6.20.23655590.9910.2441
6.2-6.80.20650600.9920.2141
6.8-7.60.15746260.9950.1621
7.6-8.770.140740.9980.1041
8.77-10.750.06234660.9990.0651
10.75-15.20.05326870.9990.0551
15.2-48.570.06614640.9980.071

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→48.565 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2699 6439 5 %
Rwork0.2385 --
obs0.2401 128770 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→48.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45256 0 0 0 45256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00346345
X-RAY DIFFRACTIONf_angle_d0.69662583
X-RAY DIFFRACTIONf_dihedral_angle_d6.92717395
X-RAY DIFFRACTIONf_chiral_restr0.0486692
X-RAY DIFFRACTIONf_plane_restr0.0047953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.43690.43972130.37534057X-RAY DIFFRACTION99
3.4369-3.47730.38332110.35814022X-RAY DIFFRACTION100
3.4773-3.51970.36582150.3214084X-RAY DIFFRACTION100
3.5197-3.56420.32762140.30224067X-RAY DIFFRACTION100
3.5642-3.61110.36152140.29684053X-RAY DIFFRACTION100
3.6111-3.66060.38752120.30964046X-RAY DIFFRACTION100
3.6606-3.71280.37362140.32264058X-RAY DIFFRACTION100
3.7128-3.76820.31432130.27924045X-RAY DIFFRACTION100
3.7682-3.82710.27852160.2734107X-RAY DIFFRACTION100
3.8271-3.88980.32012120.30184038X-RAY DIFFRACTION99
3.8898-3.95690.33512120.29914026X-RAY DIFFRACTION99
3.9569-4.02880.27612140.25764054X-RAY DIFFRACTION100
4.0288-4.10620.30982150.24964103X-RAY DIFFRACTION100
4.1062-4.190.25922130.23854030X-RAY DIFFRACTION100
4.19-4.28110.27372160.23444119X-RAY DIFFRACTION100
4.2811-4.38060.2822130.2214046X-RAY DIFFRACTION100
4.3806-4.49010.23482150.20424085X-RAY DIFFRACTION100
4.4901-4.61140.21782150.20064087X-RAY DIFFRACTION100
4.6114-4.74690.23952150.20014082X-RAY DIFFRACTION100
4.7469-4.90.21822140.19944066X-RAY DIFFRACTION100
4.9-5.0750.20312150.19634081X-RAY DIFFRACTION100
5.075-5.27790.26012150.21814093X-RAY DIFFRACTION100
5.2779-5.51780.25042160.22534095X-RAY DIFFRACTION100
5.5178-5.80830.27082130.22544055X-RAY DIFFRACTION100
5.8083-6.17150.25372170.22344117X-RAY DIFFRACTION100
6.1715-6.64690.28522160.23644104X-RAY DIFFRACTION100
6.6469-7.31380.26852160.22364096X-RAY DIFFRACTION100
7.3138-8.36750.23942170.21084127X-RAY DIFFRACTION100
8.3675-10.52450.17882170.17054110X-RAY DIFFRACTION100
10.5245-48.5650.24962210.2364178X-RAY DIFFRACTION99

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