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- PDB-7ckg: Crystal structure of TMSiPheRS complexed with TMSiPhe -

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Basic information

Entry
Database: PDB / ID: 7ckg
TitleCrystal structure of TMSiPheRS complexed with TMSiPhe
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / P-TRIMETHYSILYL PHENYLALANINE
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, type 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-type / Tyrosine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
4-(trimethylsilyl)-L-phenylalanine / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.053 Å
AuthorsSun, J.P. / Wang, J.Y. / Zhu, Z.L. / He, Q.T. / Xiao, P.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Nat Commun / Year: 2020
Title: DeSiphering receptor core-induced and ligand-dependent conformational changes in arrestin via genetic encoded trimethylsilyl 1 H-NMR probe.
Authors: Liu, Q. / He, Q.T. / Lyu, X. / Yang, F. / Zhu, Z.L. / Xiao, P. / Yang, Z. / Zhang, F. / Yang, Z.Y. / Wang, X.Y. / Sun, P. / Wang, Q.W. / Qu, C.X. / Gong, Z. / Lin, J.Y. / Xu, Z. / Song, S.L. ...Authors: Liu, Q. / He, Q.T. / Lyu, X. / Yang, F. / Zhu, Z.L. / Xiao, P. / Yang, Z. / Zhang, F. / Yang, Z.Y. / Wang, X.Y. / Sun, P. / Wang, Q.W. / Qu, C.X. / Gong, Z. / Lin, J.Y. / Xu, Z. / Song, S.L. / Huang, S.M. / Guo, S.C. / Han, M.J. / Zhu, K.K. / Chen, X. / Kahsai, A.W. / Xiao, K.H. / Kong, W. / Li, F.H. / Ruan, K. / Li, Z.J. / Yu, X. / Niu, X.G. / Jin, C.W. / Wang, J. / Sun, J.P.
History
DepositionJul 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
A: Tyrosine--tRNA ligase
B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0623
Polymers71,8252
Non-polymers2371
Water2,198122
1
A: Tyrosine--tRNA ligase

B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0623
Polymers71,8252
Non-polymers2371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area2800 Å2
ΔGint-25 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.102, 83.426, 106.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine--tRNA ligase / Tyrosyl-tRNA synthetase / TyrRS


Mass: 35912.555 Da / Num. of mol.: 2 / Mutation: Y32H,I63G,L65V,H70Q,D158G,I159G,V164G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Gene: tyrS, MJ0389 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical ChemComp-TSQ / 4-(trimethylsilyl)-L-phenylalanine


Type: L-peptide linking / Mass: 237.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO2Si / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 26% PEG 1500, 10mM Hepes, 200mM L-Proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.05→48.22 Å / Num. obs: 38466 / % possible obs: 96.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.051 / Net I/σ(I): 9.5
Reflection shellResolution: 2.05→2.11 Å / Rmerge(I) obs: 0.58 / Num. unique obs: 7278 / Rpim(I) all: 0.437

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Processing

Software
NameVersionClassification
PHENIX1.12rc0_2787refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HJR

4hjr


Resolution: 2.053→48.219 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2599 1912 4.97 %
Rwork0.2067 36524 -
obs0.2093 38436 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.11 Å2 / Biso mean: 35.0186 Å2 / Biso min: 11.61 Å2
Refinement stepCycle: final / Resolution: 2.053→48.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4950 0 16 122 5088
Biso mean--43.71 33.5 -
Num. residues----619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115094
X-RAY DIFFRACTIONf_angle_d1.0596845
X-RAY DIFFRACTIONf_chiral_restr0.069747
X-RAY DIFFRACTIONf_plane_restr0.006885
X-RAY DIFFRACTIONf_dihedral_angle_d27.2312004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.053-2.10420.36661260.3056255795
2.1042-2.16110.34041290.2568265699
2.1611-2.22460.27761590.2403263198
2.2246-2.29650.30891450.2363264998
2.2965-2.37850.29671300.2333265798
2.3785-2.47380.30341160.2467262097
2.4738-2.58630.30841230.2381263897
2.5863-2.72270.3261520.2334264698
2.7227-2.89320.29141550.2208262597
2.8932-3.11660.26751280.2226260895
3.1166-3.43020.26291340.2106256394
3.4302-3.92630.23921400.1799258394
3.9263-4.9460.2341230.1668249390
4.946-48.2190.19251520.1801259890

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