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- PDB-9qrp: Thermus thermophilus seryl-tRNA synthetase bound to tRNA(ser)(GGA... -

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Basic information

Entry
Database: PDB / ID: 9qrp
TitleThermus thermophilus seryl-tRNA synthetase bound to tRNA(ser)(GGA) and seryl-adenylate analogue.
Components
  • Serine--tRNA ligase
  • tRNA(Ser), GGA anticodon
KeywordsRNA BINDING PROTEIN / protein synthesis / aminoacyl-tRNA synthetase / tRNA
Function / homology
Function and homology information


selenocysteine biosynthetic process / serine binding / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / tRNA binding / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / 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)
Similarity search - Domain/homology
: / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE / : / RNA / RNA (> 10) / Serine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCusack, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: EMBO J / Year: 1996
Title: The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site.
Authors: Cusack, S. / Yaremchuk, A. / Tukalo, M.
#1: Journal: FEBS Lett / Year: 1992
Title: A new crystal form of the complex between seryl-tRNA synthetase and tRNA(Ser) from Thermus thermophilus that diffracts to 2.8 A resolution.
Authors: Yaremchuk, A.D. / Tukalo, M.A. / Krikliviy, I. / Malchenko, N. / Biou, V. / Berthet-Colominas, C. / Cusack, S.
History
DepositionApr 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine--tRNA ligase
B: Serine--tRNA ligase
T: tRNA(Ser), GGA anticodon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,04116
Polymers126,1593
Non-polymers1,88213
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12090 Å2
ΔGint-186 kcal/mol
Surface area45590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.040, 125.810, 117.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / RNA chain , 2 types, 3 molecules ABT

#1: Protein Serine--tRNA ligase / Seryl-tRNA synthetase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 47878.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: serS, TT_C0520 / Production host: Escherichia coli (E. coli) / References: UniProt: P34945, serine-tRNA ligase
#2: RNA chain tRNA(Ser), GGA anticodon


Mass: 30401.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Purified wild-type tRNA. Presumed modifications in T(PSI)C loop. TTH_RS04290 tRNA-Ser [ Thermus thermophilus HB8 ] Gene ID: 3168319
Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 46197919

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Non-polymers , 4 types, 227 molecules

#3: Chemical ChemComp-SSA / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE


Mass: 433.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N7O8S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.55 Å3/Da / Density % sol: 65.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 10 microliter hanging drops containing 25 mM Tris-maleate/NaOH buffer at pH 7.2,2.5 mM MgC12,20% saturated (V/V) ammonium sulphate, 1 mM NaN3, 2.6 mg/ml tRNA(ser) and 5.6 mg/ml seryl-tRNA ...Details: 10 microliter hanging drops containing 25 mM Tris-maleate/NaOH buffer at pH 7.2,2.5 mM MgC12,20% saturated (V/V) ammonium sulphate, 1 mM NaN3, 2.6 mg/ml tRNA(ser) and 5.6 mg/ml seryl-tRNA synthetase (stoichiometric ratio of 1.5 tRNA molecules to one enzyme dimer), were equil- ibrated at room temperature against 32% saturated ammonium sulphate.

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Data collection

DiffractionMean temperature: 138 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 19, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 45116 / % possible obs: 90.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 27.77 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.5
Reflection shellResolution: 2.7→2.82 Å / Rmerge(I) obs: 0.225 / Num. unique obs: 2759 / % possible all: 48.6

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.99 Å / SU ML: 0.2758 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.828
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2296 2321 5.14 %
Rwork0.1842 42795 -
obs0.1866 45116 90.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.46 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6541 1863 109 214 8727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219004
X-RAY DIFFRACTIONf_angle_d0.530512658
X-RAY DIFFRACTIONf_chiral_restr0.03431441
X-RAY DIFFRACTIONf_plane_restr0.00521305
X-RAY DIFFRACTIONf_dihedral_angle_d18.44413998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.3246660.24241032X-RAY DIFFRACTION38.11
2.76-2.810.2714680.21791486X-RAY DIFFRACTION52.93
2.81-2.880.29921460.22692672X-RAY DIFFRACTION98.19
2.88-2.950.27521480.22092701X-RAY DIFFRACTION98.41
2.95-3.030.27681490.20812703X-RAY DIFFRACTION98.65
3.03-3.120.23541520.21112716X-RAY DIFFRACTION98.42
3.12-3.220.3111230.2142697X-RAY DIFFRACTION97.88
3.22-3.340.25071770.20182699X-RAY DIFFRACTION98.36
3.34-3.470.23921340.18942725X-RAY DIFFRACTION98.25
3.47-3.620.18791320.17862711X-RAY DIFFRACTION97.63
3.63-3.810.23061540.16932692X-RAY DIFFRACTION97.37
3.82-4.050.22531570.16412715X-RAY DIFFRACTION97.19
4.05-4.360.19521430.15272675X-RAY DIFFRACTION96.54
4.36-4.80.17761640.14272662X-RAY DIFFRACTION95.73
4.8-5.480.19961230.16382674X-RAY DIFFRACTION94.3
5.48-6.850.23741350.19832644X-RAY DIFFRACTION92.76
6.85-19.990.21581500.1922591X-RAY DIFFRACTION87.85

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