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- PDB-1yfs: The crystal structure of alanyl-tRNA synthetase in complex with L... -

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Basic information

Entry
Database: PDB / ID: 1yfs
TitleThe crystal structure of alanyl-tRNA synthetase in complex with L-alanine
ComponentsAlanyl-tRNA synthetaseAlanine—tRNA ligase
KeywordsLIGASE / alpha-beta fold / helix-loop-helix motif / amino acid binding
Function / homology
Function and homology information


alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Translation protein, beta-barrel domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ALANINE / Alanine--tRNA ligase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsSwairjo, M.A. / Schimmel, P.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase.
Authors: Swairjo, M.A. / Schimmel, P.R.
#1: Journal: Mol.Cell / Year: 2004
Title: Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition
Authors: Swairjo, M.A. / Otero, F.J. / Yang, X.-L. / Lovato, M.A. / Skene, R.J. / McRee, D.E. / Ribas de Pouplana, L. / Schimmel, P.
History
DepositionJan 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alanyl-tRNA synthetase
B: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7234
Polymers107,5442
Non-polymers1782
Water6,485360
1
A: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8612
Polymers53,7721
Non-polymers891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8612
Polymers53,7721
Non-polymers891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.026, 73.868, 73.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe assymetric unit contains two biological units. The biological unit is the complex of one alanyl-tRNA synthetase molecule with one L-alanine molecule.

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Components

#1: Protein Alanyl-tRNA synthetase / Alanine—tRNA ligase / Alanine-tRNA ligase / AlaRS


Mass: 53772.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: alaS / Plasmid: PET20B+ / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O67323, alanine-tRNA ligase
#2: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: PEG 5000 mme, NaCl, Tris-Cl, Tris-base, L-alanine, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 57744

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Processing

Software
NameClassification
Blu-Icedata collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RIQ

1riq


Resolution: 2.08→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 5804 -random
Rwork0.189 ---
all0.2 57744 --
obs0.2 57744 100 %-
Displacement parametersBiso mean: 22.6 Å2
Refinement stepCycle: LAST / Resolution: 2.08→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7282 0 12 360 7654

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