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- PDB-1eov: FREE ASPARTYL-TRNA SYNTHETASE (ASPRS) (E.C. 6.1.1.12) FROM YEAST -

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Basic information

Entry
Database: PDB / ID: 1eov
TitleFREE ASPARTYL-TRNA SYNTHETASE (ASPRS) (E.C. 6.1.1.12) FROM YEAST
ComponentsASPARTYL-TRNA SYNTHETASE
KeywordsLIGASE / aminoacyl tRNA synthetase / tRNA ligase / apo-enzyme / OB-fold
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Aspartate-tRNA synthetase, type 2 / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...Aspartate-tRNA synthetase, type 2 / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Aspartate--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.3 Å
AuthorsSauter, C. / Lorber, B. / Cavarelli, J. / Moras, D. / Giege, R.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The free yeast aspartyl-tRNA synthetase differs from the tRNA(Asp)-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain.
Authors: Sauter, C. / Lorber, B. / Cavarelli, J. / Moras, D. / Giege, R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallogenesis Studies on Yeast Aspartyl-tRNA Synthetase: Use of Phase Diagram to Improve Crystal Quality.
Authors: Sauter, C. / Lorber, B. / Kern, D. / Cavarelli, J. / Moras, D. / Giege, R.
#2: Journal: Embo J. / Year: 1994
Title: The Active Site of Yeast Aspartyl-tRNA Synthetase: Structural and Functional Aspects of the Aminoacylation Reaction.
Authors: Cavarelli, J. / Eriani, G. / Rees, B. / Ruff, M. / Boeglin, M. / Mitschler, A. / Martin, F. / Gangloff, J. / Thierry, J.-C. / Moras, D.
#3: Journal: Nature / Year: 1993
Title: Yeast tRNA(Asp) Recognition by its Cognate Class II Aminoacyl-tRNA Synthetase.
Authors: Cavarelli, J. / Rees, B. / Ruff, M. / Thierry, J.-C. / Moras, D.
#4: Journal: Science / Year: 1991
Title: Class II Aminoacyl Transfer RNA Synthetases: Crystal Structure of Yeast Aspartyl-tRNA Synthetase Complexed with tRNA(Asp).
Authors: Ruff, M. / Krishnaswamy, S. / Boeglin, M. / Poterszman, A. / Mitschler, A. / Podjarny, A. / Rees, B. / Thierry, J.-C. / Moras, D.
History
DepositionMar 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASPARTYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)55,6811
Polymers55,6811
Non-polymers00
Water4,089227
1
A: ASPARTYL-TRNA SYNTHETASE

A: ASPARTYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)111,3632
Polymers111,3632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area8930 Å2
ΔGint-28 kcal/mol
Surface area40130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.230, 90.230, 184.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a homodimer constructed from chain A and a symmetry partner generated by the two-fold.

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Components

#1: Protein ASPARTYL-TRNA SYNTHETASE / ASPRS


Mass: 55681.449 Da / Num. of mol.: 1
Fragment: ENGINEERED ASPRS MONOMER LACKING THE 70 N-TERMINAL AMINO ACID RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: APS GENE / Plasmid: PTG908 / Production host: Escherichia coli (E. coli) / Strain (production host): TGE900 / References: UniProt: P04802, aspartate-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 15 MG/ML PROTEIN, 1.9 M AMMONIUM SULFATE, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 278.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
22.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.943
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Feb 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.943 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 183874 / Num. obs: 34124 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 39.7 Å2 / Rsym value: 0.082 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.277 / % possible all: 99.3
Reflection
*PLUS
Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.277

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: 1ASZ

1asz


Resolution: 2.3→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM-LIKELYHOOD TARGET USING AMPLITUDES.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2299 7 %RANDOM
Rwork0.202 ---
all0.204 34124 --
obs0.202 32837 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.29 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.22 Å20 Å20 Å2
2--3.22 Å20 Å2
3----6.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 0 0 227 4148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.35 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.277 138 6.9 %
Rwork0.236 1867 -
obs--88.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 30538
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.16

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