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- PDB-1yft: The crystal structure of the catalytic fragment of alanyl-tRNA sy... -

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Basic information

Entry
Database: PDB / ID: 1yft
TitleThe crystal structure of the catalytic fragment of alanyl-tRNA synthetase in complex wtih glycine
ComponentsAlanyl-tRNA synthetaseAlanine—tRNA ligase
KeywordsLIGASE / alpha-beta fold / amino acid binding / helix-loop helix motif
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
GLYCINE / Alanine--tRNA ligase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.23 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8472
Polymers53,7721
Non-polymers751
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Alanyl-tRNA synthetase
hetero molecules

A: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6954
Polymers107,5442
Non-polymers1502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6260 Å2
ΔGint-20 kcal/mol
Surface area35600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.912, 73.912, 172.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsthe biological unit is the entire asymmetric unit, i.e. one alanyl-tRNa synthetase molecule in complex with one glycine 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.: 1
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-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.26 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: PEG 5000 mme, NaCL, Tris-Cl, Tris-base, glycine, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.82653 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2004
RadiationMonochromator: curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82653 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 24100 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 12
Reflection shellResolution: 2.23→2.33 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.44 / % possible all: 100

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Processing

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

1riq


Resolution: 2.23→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2384 10 %random
Rwork0.207 ---
all0.21 24100 --
obs0.21 24100 --
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 2.23→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3642 0 5 193 3840
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0185
X-RAY DIFFRACTIONc_angle_deg1.431
X-RAY DIFFRACTIONc_mcbond_it0.908
X-RAY DIFFRACTIONc_mcangle_it1.222
X-RAY DIFFRACTIONc_scbond_it1.301
X-RAY DIFFRACTIONc_scangle_it1.521
LS refinement shellResolution: 2.23→2.33 Å / Rfactor Rfree error: 0.233 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.216 286 9 %
Rwork-2476 -
obs--99.3 %

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