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- PDB-9sh9: Thermus thermophilus asparaginyl-tRNA synthetase dimer with bound ATP -

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Basic information

Entry
Database: PDB / ID: 9sh9
TitleThermus thermophilus asparaginyl-tRNA synthetase dimer with bound ATP
ComponentsAsparagine--tRNA ligase
KeywordsTRANSLATION / RNA binding protein Enzyme / synthetises asparaginyl-adenylate from asparagine and ATP
Function / homology
Function and homology information


asparagine-tRNA ligase / asparagine-tRNA ligase activity / asparaginyl-tRNA aminoacylation / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
Asparagine-tRNA ligase / 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 / 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, OB-fold
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Asparagine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsCusack, S. / Seignovert, L. / Leberman, R. / Berthet-Colominas, C.
Funding support France, 1items
OrganizationGrant numberCountry
Other government France
Citation
Journal: EMBO J / Year: 1998
Title: The crystal structure of asparaginyl-tRNA synthetase from Thermus thermophilus and its complexes with ATP and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid.
Authors: Berthet-Colominas, C. / Seignovert, L. / Haertlein, M. / Grotli, M. / Cusack, S. / Leberman, R.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 1997
Title: Preliminary X-ray diffraction studies on asparaginyl-tRNA synthetase from Thermus thermophilus.
Authors: Berthet-Colominas, C. / Seignovert, L. / Cusack, S. / Leberman, R.
#2: Journal: Eur J Biochem / Year: 1996
Title: Asparaginyl-tRNA synthetase from Thermus thermophilus HB8. Sequence of the gene and crystallization of the enzyme expressed in Escherichia coli.
Authors: Seignovert, L. / Haertlein, M. / Leberman, R.
History
DepositionAug 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Asparagine--tRNA ligase
B: Asparagine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,87810
Polymers101,7182
Non-polymers1,1608
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-99 kcal/mol
Surface area33660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.954, 124.954, 246.821
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 1 - 438 / Label seq-ID: 1 - 438

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Asparagine--tRNA ligase / Asparaginyl-tRNA synthetase / AsnRS


Mass: 50858.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: asnS, TTHA0708 / Production host: Escherichia coli (E. coli) / References: UniProt: P54263, asparagine-tRNA ligase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: Native crystals grwon with protein 5 mg/ml, 12-15 % PEG 6000, 0.3M KCI at pH 8.4 Crystal soaked in 5 mM ATP and 10 mM MgCl2 for several hours, crystal phase change to new space-group with ...Details: Native crystals grwon with protein 5 mg/ml, 12-15 % PEG 6000, 0.3M KCI at pH 8.4 Crystal soaked in 5 mM ATP and 10 mM MgCl2 for several hours, crystal phase change to new space-group with dimer in asymmetric unit. Cryoprotectant 30% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.87 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 14, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.95→24.474 Å / Num. obs: 23382 / % possible obs: 94.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 9.32
Reflection shellResolution: 2.95→3.026 Å / Rmerge(I) obs: 0.271 / Num. unique obs: 1440

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→24.474 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.894 / SU B: 15.956 / SU ML: 0.292 / Cross valid method: FREE R-VALUE / ESU R Free: 0.406
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2275 1161 5.103 %
Rwork0.2039 21592 -
all0.205 --
obs-22753 91.831 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.453 Å2
Baniso -1Baniso -2Baniso -3
1--0.587 Å2-0.294 Å2-0 Å2
2---0.587 Å20 Å2
3---1.905 Å2
Refinement stepCycle: LAST / Resolution: 2.95→24.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7118 0 68 6 7192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0127388
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166913
X-RAY DIFFRACTIONr_angle_refined_deg0.8861.86810009
X-RAY DIFFRACTIONr_angle_other_deg0.3311.7715855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5165864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.538599
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.80852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.156101223
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.46710399
X-RAY DIFFRACTIONr_chiral_restr0.0430.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028973
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021885
X-RAY DIFFRACTIONr_nbd_refined0.1740.21371
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.26511
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23414
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23610
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2131
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1590.217
X-RAY DIFFRACTIONr_nbd_other0.1670.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2580.24
X-RAY DIFFRACTIONr_mcbond_it1.7714.7493465
X-RAY DIFFRACTIONr_mcbond_other1.774.7493465
X-RAY DIFFRACTIONr_mcangle_it3.1198.5334326
X-RAY DIFFRACTIONr_mcangle_other3.1198.5334327
X-RAY DIFFRACTIONr_scbond_it1.6194.9473923
X-RAY DIFFRACTIONr_scbond_other1.6194.9473923
X-RAY DIFFRACTIONr_scangle_it2.9258.9915683
X-RAY DIFFRACTIONr_scangle_other2.9248.9915684
X-RAY DIFFRACTIONr_lrange_it4.69344.4067840
X-RAY DIFFRACTIONr_lrange_other4.69344.4117841
X-RAY DIFFRACTIONr_ncsr_local_group_10.0350.0514596
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.034680.0501
12BX-RAY DIFFRACTIONLocal ncs0.034680.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.95-3.0260.304730.27413670.27517640.9320.95381.63270.235
3.026-3.1070.266680.25513670.25517170.9560.95883.5760.221
3.107-3.1960.263550.24413790.24516820.9540.96285.25560.215
3.196-3.2920.264660.24213520.24316280.9570.96387.10070.214
3.292-3.3980.379640.23813170.24315650.9260.96388.24280.213
3.398-3.5150.24830.22413220.22515500.9610.96890.64520.205
3.515-3.6450.273790.22912950.23214800.9560.96692.83780.213
3.645-3.790.233860.2112880.21214470.9590.9794.95510.196
3.79-3.9550.239750.19312440.19613680.9670.97496.41810.182
3.955-4.1420.196660.17812170.17913230.9780.97996.97660.171
4.142-4.3590.193550.17111720.17212670.9770.98196.84290.171
4.359-4.6150.173600.1711320.17112180.9790.98197.86540.174
4.615-4.9210.152490.15710580.15711340.9850.98397.6190.157
4.921-5.2970.207600.1759940.17710750.9720.98298.04650.175
5.297-5.7760.204520.1869270.1879990.9770.97897.9980.189
5.776-6.4130.241450.1988530.29120.960.97598.46490.196
6.413-7.3220.244430.197730.1938340.9660.97497.84170.193
7.322-8.7730.195380.1766660.1777190.9690.9897.91380.188
8.773-11.6790.162320.1895480.1875990.9830.9896.8280.201
11.679-24.4740.475120.4853210.4854290.8850.89777.62240.486

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