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- PDB-5t5s: A fragment of a human tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 5t5s
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 / MOLECULAR REPLACEMENT / Resolution: 2.202 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
DepositionAug 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Alanine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)23,4661
Polymers23,4661
Non-polymers00
Water2,396133
1
A: Alanine--tRNA ligase, cytoplasmic

A: Alanine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)46,9322
Polymers46,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)90.829, 136.141, 59.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 23465.920 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.: 133 / 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: 4.06 Å3/Da / Density % sol: 69.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M ammonium acetate, 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 8, 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: 2.202→75.557 Å / Num. all: 18960 / Num. obs: 16637 / % possible obs: 98.6 % / Redundancy: 7.1 % / Net I/σ(I): 11.5
Reflection shellResolution: 2.202→2.28 Å / Rmerge(I) obs: 0.109

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Processing

Software
NameVersionClassification
PHENIX(dev_2306: ???)refinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5T76

5t76


Resolution: 2.202→29.491 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 841 5.06 %
Rwork0.2083 --
obs0.2108 16634 87.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.202→29.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 0 135 1701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081593
X-RAY DIFFRACTIONf_angle_d1.0232142
X-RAY DIFFRACTIONf_dihedral_angle_d17.7091016
X-RAY DIFFRACTIONf_chiral_restr0.047250
X-RAY DIFFRACTIONf_plane_restr0.006279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2024-2.34040.3012910.28751730X-RAY DIFFRACTION59
2.3404-2.5210.28291310.24062369X-RAY DIFFRACTION80
2.521-2.77450.28441470.23212877X-RAY DIFFRACTION98
2.7745-3.17560.29141670.23562961X-RAY DIFFRACTION100
3.1756-3.99930.28221300.20912860X-RAY DIFFRACTION94
3.9993-29.49380.21161750.1692996X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 32.1008 Å / Origin y: -2.1386 Å / Origin z: 14.8135 Å
111213212223313233
T0.1601 Å2-0.0464 Å2-0.0055 Å2-0.3697 Å2-0.0118 Å2--0.2885 Å2
L0.1792 °2-0.3799 °2-0.2022 °2-2.1629 °20.3296 °2--2.5112 °2
S-0.0629 Å °0.0547 Å °-0.016 Å °0.0997 Å °0.0011 Å °0.2228 Å °0.1439 Å °-0.671 Å °0.1095 Å °
Refinement TLS groupSelection details: all

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