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- PDB-9sh8: Thermus thermophilus asparaginyl-tRNA synthetase with bound sulph... -

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Basic information

Entry
Database: PDB / ID: 9sh8
TitleThermus thermophilus asparaginyl-tRNA synthetase with bound sulphamoyl-analogue of asparaginyl-adenylate (AsnAMS)
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
5'-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE / Asparagine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3453
Polymers50,8591
Non-polymers4862
Water75742
1
A: Asparagine--tRNA ligase
hetero molecules

A: Asparagine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6896
Polymers101,7182
Non-polymers9714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area9910 Å2
ΔGint-50 kcal/mol
Surface area34430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.183, 125.183, 126.591
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 50858.855 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NSS / 5'-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE / ASN-SA


Mass: 461.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N8O8S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.81 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: Native crystals grown with protein 5 mg ml- l, 12-15 % PEG 6000, 0.3M KCI at pH 8.4. Soaked for 15 h in mother liquor containing 100 mM AsnAMS.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.89 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 2.62→14.84 Å / Num. obs: 16965 / % possible obs: 94.5 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 9.54
Reflection shellResolution: 2.62→2.69 Å / Rmerge(I) obs: 0.257 / Num. unique obs: 1073

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→14.84 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.904 / SU B: 11.486 / SU ML: 0.242 / Cross valid method: FREE R-VALUE / ESU R: 1.525 / ESU R Free: 0.372
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2726 1717 10.123 %
Rwork0.209 15245 -
all0.215 --
obs-16962 93.352 %
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: 57.357 Å2
Baniso -1Baniso -2Baniso -3
1--1.168 Å2-0.584 Å2-0 Å2
2---1.168 Å20 Å2
3---3.79 Å2
Refinement stepCycle: LAST / Resolution: 2.62→14.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3593 0 32 42 3667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0123735
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.8785060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9415439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.576550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89310618
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.60410201
X-RAY DIFFRACTIONr_chiral_restr0.0840.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022942
X-RAY DIFFRACTIONr_nbd_refined0.1850.21371
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22444
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2101
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1160.2126
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0560.214
X-RAY DIFFRACTIONr_mcbond_it2.095.6231759
X-RAY DIFFRACTIONr_mcangle_it3.55310.1192197
X-RAY DIFFRACTIONr_scbond_it2.3585.8191976
X-RAY DIFFRACTIONr_scangle_it4.00610.5982863
X-RAY DIFFRACTIONr_lrange_it6.84361.3775183
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
2.62-2.6860.4191420.2959770.3112610.9190.95288.73910.251
2.686-2.7570.3541160.25210790.2612410.9280.96396.29330.216
2.757-2.8340.3871220.27810440.2912070.9210.95496.60310.241
2.834-2.9180.3411080.27910360.28511860.9330.9596.45870.244
2.918-3.010.3551070.299860.29711400.9120.9595.87720.254
3.01-3.1110.3251030.279620.27511060.9330.95296.29290.248
3.111-3.2230.3531140.2659270.27410820.9210.95696.21070.242
3.223-3.3480.3271030.2418800.24910310.9320.96395.34430.228
3.348-3.4890.3011030.2568620.26110070.940.95795.82920.246
3.489-3.6490.283810.2238260.2289610.9360.96894.38090.218
3.649-3.8340.241840.2137880.2169190.9590.96994.88570.215
3.834-4.0490.25850.2017490.2068850.960.97394.23730.208
4.049-4.3060.249810.1896780.1968300.9610.97791.44580.208
4.306-4.6190.226640.1766470.187850.9650.98190.57320.201
4.619-5.0110.237670.1545960.1627310.9690.98590.69770.186
5.011-5.5250.25560.1635660.176740.9620.98292.28490.198
5.525-6.2370.23640.1635110.176190.9680.98292.89180.192
6.237-7.3220.223470.1644560.1695430.9640.98292.63350.195
7.322-9.2860.223460.1613750.1684630.9680.98490.92870.205
9.286-14.840.161240.1853000.1833570.9890.97990.75630.203

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