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- PDB-1l0w: Aspartyl-tRNA synthetase-1 from space-grown crystals -

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Basic information

Entry
Database: PDB / ID: 1l0w
TitleAspartyl-tRNA synthetase-1 from space-grown crystals
ComponentsAspartyl-tRNA synthetase
KeywordsLIGASE / Space-grown crystal / dimeric enzyme / flexible domains
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
GAD-like domain / : / : / Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) ...GAD-like domain / : / : / Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / 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. / Gyrase A; domain 2 / 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(Asp) ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsNg, J.D. / Sauter, C. / Lorber, B. / Kirkland, N. / Arnez, J. / Giege, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Comparative analysis of space-grown and earth-grown crystals of an aminoacyl-tRNA synthetase: space-grown crystals are more useful for structural determination.
Authors: Ng, J.D. / Sauter, C. / Lorber, B. / Kirkland, N. / Arnez, J. / Giege, R.
History
DepositionFeb 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartyl-tRNA synthetase
B: Aspartyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)132,2502
Polymers132,2502
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-47 kcal/mol
Surface area49080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.020, 156.100, 177.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aspartyl-tRNA synthetase / ASPARTYL-TRNA SYNTHETASE-1 / AspRS-1 / AspRS / Aspartate--tRNA ligase


Mass: 66124.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P36419, aspartate-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.21 %
Crystal growTemperature: 298 K / Method: under microgravity / pH: 7.5
Details: Ammonium sulfate, Tris-HCl, EDTA, DTT, PMSF, pH 7.5, Under microgravity, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
22.2 Mammonium sulfate1drop
325 mMTris-HCl1droppH7.5
410 mMEDTA1drop
51 mMdithiothreitol1drop
60.01 %(m/v)PMSF1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 25, 1996 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 100854 / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 2.16 / % possible all: 77.9
Reflection
*PLUS
Lowest resolution: 12 Å / % possible obs: 93.3 % / Num. measured all: 320200
Reflection shell
*PLUS
% possible obs: 95.3 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→11.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2684000.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE NUMBER OF RELECTIONS LISTED, 81861, WERE THE NUMBER IN COMMON WITH THE EARTH DATA SET USED IN THE COMPARATIVE INVESTIGATION OF SPACE VS. EARTH DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2438 3 %RANDOM
Rwork0.217 ---
obs-81861 70.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.2237 Å2 / ksol: 0.412551 e/Å3
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1-6.81 Å20 Å20 Å2
2---8.72 Å20 Å2
3---1.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.01→11.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9334 0 0 187 9521
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.18
LS refinement shellResolution: 2.01→2.12 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 299 3 %
Rwork0.245 9612 -
obs--51.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.18
LS refinement shell
*PLUS
Rfactor obs: 0.245

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