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- PDB-1f7v: CRYSTAL STRUCTURE OF YEAST ARGINYL-TRNA SYNTHETASE COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 1f7v
TitleCRYSTAL STRUCTURE OF YEAST ARGINYL-TRNA SYNTHETASE COMPLEXED WITH THE TRNAARG
Components
  • ARGINYL-TRNA SYNTHETASE
  • TRNA(ARG)
KeywordsLIGASE/RNA / tRNA-protein complex / aminoacylation / arginyl-tRNA synthetase / LIGASE-RNA COMPLEX
Function / homology
Function and homology information


arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / sequence-specific mRNA binding / mitochondrial translation / mitochondrion / ATP binding / cytosol
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), catalytic domain / 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), catalytic domain / 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
RNA / RNA (> 10) / Arginine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsDelagoutte, B. / Moras, D. / Cavarelli, J.
Citation
Journal: EMBO J. / Year: 2000
Title: tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding
Authors: Delagoutte, B. / Moras, D. / Cavarelli, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase - yeast tRNAArg complexes
Authors: Delagoutte, B. / Keith, G. / Moras, D. / Cavarelli, J.
History
DepositionJun 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: TRNA(ARG)
A: ARGINYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)94,1922
Polymers94,1922
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.721, 129.606, 184.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222

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Components

#1: RNA chain TRNA(ARG)


Mass: 24573.770 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: this sequence occurs naturally in yeast Saccharomyces cerevisae
#2: Protein ARGINYL-TRNA SYNTHETASE / E.C.6.1.1.19 / CYTOPLASMIC ARGININE-TRNA LIGASE / ARGRS


Mass: 69617.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PTRC99 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05506, arginine-tRNA ligase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.41 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.1 M (NH4)2SO4, hexanediol, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1hexanediol11
2(NH4)2SO411
3(NH4)2SO412
Crystal grow
*PLUS
Details: Delagoutte, B., (2000) Acta Crystallogr., Sect.D, 56, 492.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlArgRS1drop
23.8 mg/mltRNA1drop
310 mMATP1drop
415 mM1dropMgSO4
52.1 Mammonium sulfate1reservoir
63.5 %1,6-hexanediol1reservoir
7100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. all: 28856 / Num. obs: 28856 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 56.9 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 30.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.262 / Num. unique all: 2835 / % possible all: 100
Reflection
*PLUS

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementResolution: 2.9→24.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2531107.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2875 10 %RANDOM
Rwork0.194 ---
obs0.194 28856 99.9 %-
all-28856 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.52 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso mean: 39.4 Å2
Baniso -1Baniso -2Baniso -3
1--8.06 Å20 Å20 Å2
2---12.87 Å20 Å2
3---20.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.9→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4892 1567 0 44 6503
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.881.5
X-RAY DIFFRACTIONc_mcangle_it5.682
X-RAY DIFFRACTIONc_scbond_it5.712
X-RAY DIFFRACTIONc_scangle_it7.72.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 498 10.5 %
Rwork0.295 4238 -
obs--99.8 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.36 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.295

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