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- PDB-1bs2: YEAST ARGINYL-TRNA SYNTHETASE -

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Basic information

Entry
Database: PDB / ID: 1bs2
TitleYEAST ARGINYL-TRNA SYNTHETASE
ComponentsPROTEIN (ARGINYL-TRNA SYNTHETASE)
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS
Function / homology
Function and homology information


arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / 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) / 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 / Arginine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.75 Å
AuthorsCavarelli, J. / Delagouute, B. / Eriani, G. / Gangloff, J. / Moras, D.
CitationJournal: EMBO J. / Year: 1998
Title: L-arginine recognition by yeast arginyl-tRNA synthetase.
Authors: Cavarelli, J. / Delagoutte, B. / Eriani, G. / Gangloff, J. / Moras, D.
History
DepositionAug 31, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (ARGINYL-TRNA SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7932
Polymers69,6181
Non-polymers1751
Water4,882271
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.374, 100.374, 204.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (ARGINYL-TRNA SYNTHETASE) / E.C.6.1.1.19 LIGASE / ARGRS / ARGININE - TRNA LIGASE


Mass: 69617.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: YEAST GENOME, CHROMOSOME IV, OPEN READING FRAME YDR341C, ACCESSION NUMBER S70106
Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: Q05506, arginine-tRNA ligase
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / Details: THE AMINO ACID WAS CHEMICALLY SYNTHESIZED
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 63 %
Crystal growpH: 7
Details: AMMONIUM SULFATE 2.45 M, 100MM TRIS-HCL, PH 7.0 AT 290K
Crystal
*PLUS
Density % sol: 63 %
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.45 Mammonium sulfate1reservoir
2100 mMTris-HCl1reservoir
313.5 mg/mlprotein1drop
45 mML-arginine1drop
55 mMATP1drop
610 mM1dropMgSO4
750 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.1024
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1024 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 27890 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 42.1 Å2 / Rsym value: 0.042 / Net I/σ(I): 35
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 7.3 / Rsym value: 0.181 / % possible all: 96
Reflection
*PLUS
Num. measured all: 168917 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 80 % / Num. unique obs: 2660 / Num. measured obs: 12392 / Rmerge(I) obs: 0.18

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Processing

Software
NameVersionClassification
CCP4model building
CNS0.1-0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.75→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 5235707.2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2030 7.5 %RANDOM
Rwork0.207 ---
obs0.207 27116 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.07 Å2 / ksol: 0.285 e/Å3
Displacement parametersBiso mean: 55.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.36 Å20 Å20 Å2
2--8.36 Å20 Å2
3----16.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4874 0 12 271 5157
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_d20.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.871.5
X-RAY DIFFRACTIONc_mcangle_it5.822
X-RAY DIFFRACTIONc_scbond_it6.372
X-RAY DIFFRACTIONc_scangle_it8.622.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 322 7.6 %
Rwork0.31 3890 -
obs--92.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.1-0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 55.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
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: 0.382 / % reflection Rfree: 7.6 % / Rfactor Rwork: 0.31

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