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- PDB-1n9w: Crystal structure of the non-discriminating and archaeal-type asp... -

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Basic information

Entry
Database: PDB / ID: 1n9w
TitleCrystal structure of the non-discriminating and archaeal-type aspartyl-tRNA synthetase from Thermus thermophilus
Componentsaspartyl-tRNA synthetase 2
KeywordsBIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


aspartate-tRNAAsn ligase / aspartate-tRNA(Asn) ligase activity / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / nucleic acid binding / ATP binding / 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(Asp/Asn) ligase / Aspartate--tRNA(Asp/Asn) ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCharron, C. / Roy, H. / Blaise, M. / Giege, R. / Kern, D.
Citation
Journal: EMBO J. / Year: 2003
Title: Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain
Authors: Charron, C. / Roy, H. / Blaise, M. / Giege, R. / Kern, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary X-ray diffraction data of the second and archaebacterial-type aspartyl-tRNA synthetase from Thermus thermophilus
Authors: Charron, C. / Roy, H. / Lorber, L. / Kern, D. / Giege, R.
History
DepositionNov 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: 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 / database_2
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 2
B: aspartyl-tRNA synthetase 2


Theoretical massNumber of molelcules
Total (without water)96,7952
Polymers96,7952
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-31 kcal/mol
Surface area29830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.361, 122.554, 167.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer in the asymmetric unit

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Components

#1: Protein aspartyl-tRNA synthetase 2


Mass: 48397.262 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: Q9LCY8, UniProt: Q5SIC2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 8000 and NaCl, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 %(v/v)PEG80001reservoir
2100 mMCHES1droppH9.5
3200 mM1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 53223 / Num. obs: 52274 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.045 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.221 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.221

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 3443 RANDOM
Rwork0.227 --
all0.227 53223 -
obs0.227 52274 -
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5762 0 0 159 5921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.227
LS refinement shellResolution: 2.3→2.36 Å
RfactorNum. reflection
Rfree0.296 220
Rwork0.257 -
obs-3243
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 45048 / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.2
LS refinement shell
*PLUS
Highest resolution: 2.3 Å

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