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- PDB-1qu2: INSIGHTS INTO EDITING FROM AN ILE-TRNA SYNTHETASE STRUCTURE WITH ... -

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Entry
Database: PDB / ID: 1qu2
TitleINSIGHTS INTO EDITING FROM AN ILE-TRNA SYNTHETASE STRUCTURE WITH TRNA(ILE) AND MUPIROCIN
Components
  • ISOLEUCYL-TRNA
  • ISOLEUCYL-TRNA SYNTHETASEAminoacyl tRNA synthetase
KeywordsLIGASE/RNA / PROTEIN-RNA COMPLEX / METAL IONS / EDITING TRNA SYNTHETASE / DOUBLE-SIEVE / LIGASE-RNA COMPLEX
Function / homologyValyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Rossmann-like alpha/beta/alpha sandwich fold / Aminoacyl-transfer RNA synthetases class-I signature. / Anticodon-binding domain of tRNA / Zinc finger found in FPG and IleRS / tRNA synthetases class I (I, L, M and V) / Isoleucyl tRNA synthetase type 1, anticodon-binding domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-tRNA synthetase, class Ia / Isoleucine-tRNA ligase ...Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Rossmann-like alpha/beta/alpha sandwich fold / Aminoacyl-transfer RNA synthetases class-I signature. / Anticodon-binding domain of tRNA / Zinc finger found in FPG and IleRS / tRNA synthetases class I (I, L, M and V) / Isoleucyl tRNA synthetase type 1, anticodon-binding domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-tRNA synthetase, class Ia / Isoleucine-tRNA ligase / Isoleucine-tRNA ligase, type 1 / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Zinc finger, FPG/IleRS-type / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / isoleucyl-tRNA aminoacylation / isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm / Isoleucine--tRNA ligase
Function and homology information
Specimen sourceStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsSilvian, L.F. / Wang, J. / Steitz, T.A.
Citation
Journal: Science / Year: 1999
Title: Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin.
Authors: Silvian, L.F. / Wang, J. / Steitz, T.A.
#1: Journal: To be Published
Title: Metal Ions that Stabilize the tRNA and Mediate the Recognition by its Cognate Synthetase
Authors: Wang, J. / Silvian, L.F. / Steitz, T.A.
#2: Journal: To be Published
Title: Switching from a Resting to Synthetic and Hydrolytic Modes in Editing tRNA Synthetases
Authors: Wang, J. / Silvian, L.F. / Steitz, T.A.
#3: Journal: To be Published
Title: Structure Based Drug Design Against Mupirocin Resistant Staphylococcus Aureus
Authors: Wang, J. / Silvian, L.F. / Steitz, T.A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 6, 1999 / Release: Aug 31, 1999
RevisionDateData content typeGroupProviderType
1.0Aug 31, 1999Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
T: ISOLEUCYL-TRNA
A: ISOLEUCYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,20716
Polyers129,2942
Non-polymers91414
Water5,909328
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)71.000, 100.000, 186.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP 21 21 21

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Components

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RNA chain / Protein/peptide , 2 types, 2 molecules TA

#1: RNA chain ISOLEUCYL-TRNA


Mass: 24236.381 Da / Num. of mol.: 1 / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide ISOLEUCYL-TRNA SYNTHETASE / Aminoacyl tRNA synthetase / E.C.6.1.1.5 / ISOLEUCINE--TRNA LIGASE / ILERS


Mass: 105057.336 Da / Num. of mol.: 1 / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P41972, isoleucine-tRNA ligase

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Non-polymers , 5 types, 342 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Formula: K / Potassium
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Formula: Mg / Magnesium
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc
#6: Chemical ChemComp-MRC / MUPIROCIN / PSEUDOMONIC ACID


Mass: 500.622 Da / Num. of mol.: 1 / Formula: C26H44O9 / Mupirocin
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Formula: H2O / Water

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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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growMethod: evaporation / Details: EVAPORATION
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-IDChemical formula
10.050 mMIleRSdrop
20.050 mMtRNAdrop
31 mMMupirocindrop
412 %PEG6000reservoir
50.3 MreservoirKCl
6100 mMsodium cacodylatereservoir
7100 mMreservoirMgSO4
82 mMreservoirZnCl2
90.1 %beta-octyl glucopyranosidereservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.94
DetectorType: PRINCETON 2K / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.2→500 Å / Num. all: 67758 / Num. obs: 67758 / % possible obs: 89.1 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.3 Å2 / Rsym value: 0.079
Reflection
*PLUS
Rmerge(I) obs: 0.079

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 350319.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.28125445 %RANDOM
Rwork0.239---
obs0.2395092475.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.64 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.63 Å20 Å20 Å2
2---3.85 Å20 Å2
3----1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms74071603912859386
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg1.6
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d21.2
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d1.06
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it1.071.5
c_mcangle_it1.762
c_scbond_it1.642
c_scangle_it2.42.5
Refine LS shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3313095.2 %
Rwork0.2755612-
obs--53.6 %
Xplor file

Refinement-ID: X-RAY DIFFRACTION

Serial noParam fileTopol file
1PROTEIN_REP.PAPROTEIN.TOP
2DNA-RNA_REP.PADNA-RNA.TOP
3WATER_REP.PARAWATER.TOP
4XPLOR_PAIRS_STUF
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06

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