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- PDB-1iq0: THERMUS THERMOPHILUS ARGINYL-TRNA SYNTHETASE -

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Basic information

Entry
Database: PDB / ID: 1iq0
TitleTHERMUS THERMOPHILUS ARGINYL-TRNA SYNTHETASE
ComponentsARGINYL-TRNA SYNTHETASE
KeywordsLIGASE / arginyl-tRNA synthetase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Arginyl tRNA synthetase N-terminal domain / Arginine-tRNA ligase / Arginyl tRNA synthetase N-terminal domain / Arginyl-tRNA synthetase, catalytic core domain / Arginyl tRNA synthetase N-terminal domain superfamily / tRNA synthetases class I (R) / Arginyl tRNA synthetase N terminal domain / DALR anticodon binding domain / Arginyl tRNA synthetase N terminal dom / DALR anticodon binding ...Arginyl tRNA synthetase N-terminal domain / Arginine-tRNA ligase / Arginyl tRNA synthetase N-terminal domain / Arginyl-tRNA synthetase, catalytic core domain / Arginyl tRNA synthetase N-terminal domain superfamily / tRNA synthetases class I (R) / Arginyl tRNA synthetase N terminal domain / DALR anticodon binding domain / Arginyl tRNA synthetase N terminal dom / DALR anticodon binding / DALR anticodon binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Gyrase A; domain 2 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Arginine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsShimada, A. / Nureki, O. / Goto, M. / Takahashi, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase.
Authors: Shimada, A. / Nureki, O. / Goto, M. / Takahashi, S. / Yokoyama, S.
History
DepositionMay 24, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2001Provider: 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 / 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: ARGINYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)66,3161
Polymers66,3161
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.747, 154.747, 84.573
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein ARGINYL-TRNA SYNTHETASE


Mass: 66315.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ARGS / Plasmid: PK7 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: Q93RP5, arginine-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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

CrystalDensity Matthews: 4.41 Å3/Da / Density % sol: 72.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG8000, ethylene glycol, polyvinylpyrrolidone K15, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Shimada, A., (2001) Acta Crystallogr., D57, 272.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMHEPES1droppH7.0
210 %(v/v)PEG80001drop
38 %(v/v)ethylene glycol1drop
42.5 %polyvinylpyrrolidone150001drop
58 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 51404 / Num. obs: 49236 / % possible obs: 95.8 % / Observed criterion σ(F): 0.1 / Observed criterion σ(I): 0 / Redundancy: 7.94 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 35.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.54 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 7.4 / % possible all: 94.3

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.3→44.67 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2102404.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2467 5 %RANDOM
Rwork0.215 ---
obs0.215 49220 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.71 Å2 / ksol: 0.405 e/Å3
Displacement parametersBiso mean: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.49 Å21.26 Å20 Å2
2---3.49 Å20 Å2
3---6.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4646 0 0 196 4842
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.181.5
X-RAY DIFFRACTIONc_mcangle_it8.212
X-RAY DIFFRACTIONc_scbond_it6.752
X-RAY DIFFRACTIONc_scangle_it10.052.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 398 4.9 %
Rwork0.232 7672 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0058
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.78
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
X-RAY DIFFRACTIONc_mcbond_it5.181.5
X-RAY DIFFRACTIONc_scbond_it6.752
X-RAY DIFFRACTIONc_mcangle_it8.212
X-RAY DIFFRACTIONc_scangle_it10.052.5
LS refinement shell
*PLUS
Lowest resolution: 2.38 Å / Rfactor Rfree: 0.263 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.232 / Rfactor obs: 0.233

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