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- PDB-7f6w: Crystal structure of Saccharomyces cerevisiae lysyl-tRNA Synthetase -

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Basic information

Entry
Database: PDB / ID: 7f6w
TitleCrystal structure of Saccharomyces cerevisiae lysyl-tRNA Synthetase
ComponentsLysine--tRNA ligase
KeywordsLIGASE / Lysine-tRNA ligase / protein translation enzyme
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / Chem-PG6 / Lysine--tRNA ligase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.607 Å
AuthorsWu, S. / Li, P. / Hei, Z. / Zheng, L. / Wang, J. / Fang, P.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977107 China
National Natural Science Foundation of China (NSFC)21977108 China
National Natural Science Foundation of China (NSFC)21778067 China
National Natural Science Foundation of China (NSFC)21778064 China
CitationJournal: Cell.Mol.Life Sci. / Year: 2022
Title: Human lysyl-tRNA synthetase evolves a dynamic structure that can be stabilized by forming complex.
Authors: Wu, S. / Zheng, L. / Hei, Z. / Zhou, J.B. / Li, G. / Li, P. / Wang, J. / Ali, H. / Zhou, X.L. / Wang, J. / Fang, P.
History
DepositionJun 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5383
Polymers60,7971
Non-polymers7412
Water5,567309
1
A: Lysine--tRNA ligase
hetero molecules

A: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,0766
Polymers121,5942
Non-polymers1,4824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11120 Å2
ΔGint-32 kcal/mol
Surface area40660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.100, 111.100, 239.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Lysine--tRNA ligase / Lysyl-tRNA synthetase


Mass: 60797.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCP684_0001024300 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6V8RZ07, lysine-tRNA ligase
#2: Chemical ChemComp-KAA / 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / 5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE


Mass: 474.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N8O7S
#3: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 6.07 Å3/Da / Density % sol: 79.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Sodium HEPES, PEG 500 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→48.65 Å / Num. obs: 46870 / % possible obs: 99.8 % / Redundancy: 12.8 % / Biso Wilson estimate: 53.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.033 / Rrim(I) all: 0.117 / Net I/σ(I): 15.8 / Num. measured all: 600863 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.6912.92.2025845645150.7850.6342.2931.699.7
10.07-48.659.70.03290679300.9990.010.03340.298.7

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bju

3bju


Resolution: 2.607→18.486 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2034 1992 5.3 %
Rwork0.1724 35558 -
obs0.1741 37550 80.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.03 Å2 / Biso mean: 57.0008 Å2 / Biso min: 22.99 Å2
Refinement stepCycle: final / Resolution: 2.607→18.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4059 0 50 309 4418
Biso mean--60.31 69.71 -
Num. residues----506
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.61-2.67170.4566110.30072097
2.6717-2.74380.3489340.241260120
2.7438-2.82420.3327630.2508110736
2.8242-2.9150.31371170.2615209567
2.915-3.01880.28341720.26283070100
3.0188-3.13910.27951740.24093109100
3.1391-3.28120.24181740.22493098100
3.2812-3.45320.23151730.20063114100
3.4532-3.66790.21381750.17673127100
3.6679-3.94860.1781750.15713110100
3.9486-4.34130.18821770.13543152100
4.3413-4.95890.15531770.12193170100
4.9589-6.20810.16451800.16453223100
6.2081-18.4860.19641900.15963373100
Refinement TLS params.Method: refined / Origin x: 31.4037 Å / Origin y: 31.4511 Å / Origin z: 12.3402 Å
111213212223313233
T0.3454 Å2-0.1086 Å20.0333 Å2-0.3244 Å2-0.0274 Å2--0.246 Å2
L1.0092 °2-0.5927 °20.0353 °2-1.1214 °2-0.0448 °2--0.5683 °2
S-0.0781 Å °-0.1799 Å °-0.0257 Å °0.1587 Å °0.0294 Å °0.0365 Å °0.0267 Å °-0.0335 Å °0.0485 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA69 - 701
2X-RAY DIFFRACTION1allS1 - 357

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