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- PDB-5t76: A fragment of a human tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 5t76
TitleA fragment of a human tRNA synthetase
ComponentsAlanine--tRNA ligase, cytoplasmic
KeywordsTRANSLATION / tRNA synthetase
Function / homology
Function and homology information


regulation of cytoplasmic translational fidelity / Ser-tRNA(Ala) hydrolase activity / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / cerebellar Purkinje cell layer development / Cytosolic tRNA aminoacylation / tRNA modification / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity ...regulation of cytoplasmic translational fidelity / Ser-tRNA(Ala) hydrolase activity / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / cerebellar Purkinje cell layer development / Cytosolic tRNA aminoacylation / tRNA modification / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / tRNA processing / amino acid binding / neuromuscular process controlling balance / neuron apoptotic process / negative regulation of neuron apoptotic process / tRNA binding / mitochondrion / zinc ion binding / extracellular exosome / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
Alanine-tRNA ligase, eukaryota/bacteria / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain ...Alanine-tRNA ligase, eukaryota/bacteria / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / DHHA1 domain / DHHA1 domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Translation protein, beta-barrel domain superfamily
Similarity search - Domain/homology
Alanine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSun, L. / Schimmel, P.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Two crystal structures reveal design for repurposing the C-Ala domain of human AlaRS.
Authors: Sun, L. / Song, Y. / Blocquel, D. / Yang, X.L. / Schimmel, P.
History
DepositionSep 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alanine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)23,7471
Polymers23,7471
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.645, 38.449, 62.471
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alanine--tRNA ligase, cytoplasmic / Alanyl-tRNA synthetase / AlaRS / Renal carcinoma antigen NY-REN-42


Mass: 23747.289 Da / Num. of mol.: 1 / Fragment: UNP residues 757-965
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AARS
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P49588, alanine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 13269 / % possible obs: 99.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 16.7
Reflection shellResolution: 2→2.052 Å

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Processing

Software
NameClassification
REFMACrefinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2576 649 -
Rwork0.2146 --
obs-12323 99.5 %
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 0 157 1731
LS refinement shellResolution: 2→2.052 Å

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