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- PDB-1iyw: Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-t... -

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Basic information

Entry
Database: PDB / ID: 1iyw
TitlePreliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase
ComponentsValyl-tRNA Synthetase
KeywordsLIGASE / Rossmann Fold / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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
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 / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / 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 ...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 / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / 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. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsFukai, S. / Nureki, O. / Sekine, S. / Shimada, A. / Vassylyev, D.G. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: RNA / Year: 2003
Title: Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
Authors: Fukai, S. / Nureki, O. / Sekine, S. / Shimada, A. / Vassylyev, D.G. / Yokoyama, S.
History
DepositionSep 10, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: Valyl-tRNA Synthetase
B: Valyl-tRNA Synthetase


Theoretical massNumber of molelcules
Total (without water)197,8292
Polymers197,8292
Non-polymers00
Water0
1
A: Valyl-tRNA Synthetase


Theoretical massNumber of molelcules
Total (without water)98,9141
Polymers98,9141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Valyl-tRNA Synthetase


Theoretical massNumber of molelcules
Total (without water)98,9141
Polymers98,9141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.562, 207.328, 59.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Valyl-tRNA Synthetase / Coordinate model: Cα atoms only


Mass: 98914.445 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: P96142, valine-tRNA ligase

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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: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG4000, isopropanol, lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD PX210 / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. all: 65363 / Num. obs: 65363 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / Net I/σ(I): 7
Reflection shellResolution: 4→4.07 Å / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.4 / Num. unique all: 872 / Rsym value: 0.396 / % possible all: 89.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The coordinates for only the alpha carbons are present in the structure. THE NUMBER OF MISSING atoms WAS SO MUCH THAT REMARK 470 FOR THE MISSING atoms LIST WERE REMOVED.
RfactorNum. reflectionSelection details
Rfree0.3828 854 RANDOM
Rwork0.3164 --
all0.3196 17584 -
obs0.3196 17584 -
Refine analyze
FreeObs
Luzzati coordinate error0.81 Å0.59 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.77 Å
Refinement stepCycle: LAST / Resolution: 4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 0 0 1724
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.21
LS refinement shellResolution: 4→4.23 Å / Rfactor Rfree error: 0.032
RfactorNum. reflection% reflection
Rfree0.36 129 -
Rwork0.322 --
obs-2801 90.2 %

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