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- PDB-1ivs: CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE C... -

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Basic information

Entry
Database: PDB / ID: 1ivs
TitleCRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE
Components
  • Valyl-tRNA synthetase
  • tRNA (Val)
KeywordsLIGASE/RNA / Rossmann fold / helix bundle / coiled coil / beta barrel / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / LIGASE-RNA COMPLEX
Function / homology
Function and homology information


valine-tRNA ligase / valine-tRNA ligase activity / valyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Valyl-trna Synthetase; Chain: A, domain 4 / Valyl-trna Synthetase; Chain: A, domain 4 - #10 / Valyl-tRNA synthetase, C-terminal domain / Valine-tRNA ligase / Valyl-tRNA synthetase, tRNA-binding arm / Valyl tRNA synthetase, anticodon-binding domain / Valyl tRNA synthetase tRNA binding arm / Valyl-tRNA synthetase, tRNA-binding arm superfamily / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain ...Valyl-trna Synthetase; Chain: A, domain 4 / Valyl-trna Synthetase; Chain: A, domain 4 - #10 / Valyl-tRNA synthetase, C-terminal domain / Valine-tRNA ligase / Valyl-tRNA synthetase, tRNA-binding arm / Valyl tRNA synthetase, anticodon-binding domain / Valyl tRNA synthetase tRNA binding arm / Valyl-tRNA synthetase, tRNA-binding arm superfamily / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Helix Hairpins / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE / RNA / RNA (> 10) / Valine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å
AuthorsFukai, S. / Nureki, O. / Sekine, S.-I. / Shimada, A. / Vassylyev, D.G. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: RNA / Year: 2003
Title: Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
Authors: Fukai, S. / Nureki, O. / Sekine, S.-I. / Shimada, A. / Vassylyev, D.G. / Yokoyama, S.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: STRUCTURAL BASIS FOR DOUBLE-SIEVE DISCRIMINATION OF L-VALINE FROM L-ISOLEUCINE AND L-THREONINE BY THE COMPLEX OF TRNA(VAL) AND VALYL-TRNA SYNTHETASE
Authors: Fukai, S. / Nureki, O. / Sekine, S. / Shimada, A. / Tao, J. / Vassylyev, D.G. / Yokoyama, S.
History
DepositionMar 29, 2002Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: tRNA (Val)
D: tRNA (Val)
A: Valyl-tRNA synthetase
B: Valyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,0676
Polymers246,1784
Non-polymers8892
Water3,927218
1
C: tRNA (Val)
A: Valyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5333
Polymers123,0892
Non-polymers4441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: tRNA (Val)
B: Valyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5333
Polymers123,0892
Non-polymers4441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)411.810, 411.810, 81.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: RNA chain tRNA (Val)


Mass: 24174.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: tRNA (Val) with the CAC anticodon
#2: Protein Valyl-tRNA synthetase / Valine-tRNA ligase / ValRS


Mass: 98914.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: valS / Plasmid: pK7 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P96142, valine-tRNA ligase
#3: Chemical ChemComp-VAA / N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE


Mass: 444.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N8O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Sulfate, Magnesium Sulfate, Cacodylate Na, 1,8-diaminooctane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Details: Fukai, S., (2000) Cell (Cambridge,Mass.), 103, 793.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 mg/mlprotein1drop
250 mMsodium cacodylate1drop
31.0 Mammonium sulfate1drop
410 mMmagnesium sulfate1drop
56 %1,8-diaminooctane1drop
650 mMsodium cacodylate1reservoir
72.8 Mammonium sulfate1reservoir
810 mMmagnesium sulfate1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 24, 1998
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 150310 / Num. obs: 150310 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 56.5 Å2
Reflection shellResolution: 2.9→3.08 Å / % possible all: 87.9
Reflection
*PLUS

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.9→40 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 7532 5 %RANDOM
Rwork0.248 ---
obs0.248 150310 96.5 %-
all-150310 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.6469 Å2 / ksol: 0.297208 e/Å3
Displacement parametersBiso mean: 50.8 Å2
Baniso -1Baniso -2Baniso -3
1-8.51 Å20 Å20 Å2
2--8.51 Å20 Å2
3----17.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.77 Å
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13940 3206 60 218 17424
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_mcbond_it2.563
X-RAY DIFFRACTIONc_mcangle_it4.24
X-RAY DIFFRACTIONc_scbond_it3.624
X-RAY DIFFRACTIONc_scangle_it5.665
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 1136 5 %
Rwork0.376 21386 -
obs--87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4VAA.PARVAA.TOP
X-RAY DIFFRACTION5WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.9 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.16

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