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- PDB-1h3n: Leucyl-tRNA synthetase from Thermus thermophilus complexed with a... -

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Basic information

Entry
Database: PDB / ID: 1h3n
TitleLeucyl-tRNA synthetase from Thermus thermophilus complexed with a sulphamoyl analogue of leucyl-adenylate
ComponentsLEUCYL-TRNA SYNTHETASE
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / CLASS I AMINOACYL-TRNA SYNTHETASE / ATP + L-LEUCINE + TRNA (LEU) -> AMP + PPI + L-LEUCYL-TRNA(LEU)
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Leucyl-tRNA synthetase, domain 3 / Leucyl-tRNA synthetase, domain 3 / Leucyl-tRNA synthetase, domain 3 / Leucine-tRNA synthetase-specific domain / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Isoleucyl-tRNA Synthetase; Domain 1 ...Leucyl-tRNA synthetase, domain 3 / Leucyl-tRNA synthetase, domain 3 / Leucyl-tRNA synthetase, domain 3 / Leucine-tRNA synthetase-specific domain / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / 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 / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Roll / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
LEUCINE / Chem-LMS / Leucine--tRNA ligase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsCusack, S. / Yaremchuk, A. / Tukalo, M.
Citation
Journal: Embo J. / Year: 2000
Title: The 2A Structure of Leucyl-tRNA Synthetase and its Complex with a Leucyl-Adenylate Analogue
Authors: Cusack, S. / Yaremchuk, A. / Tukalo, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary Crystallographic Analysis of Thermus Thermophilus Leucyl-tRNA Synthetase and its Complexes with Leucine and a Non-Hydrolysable Leucyl-Adenylate Analogue
Authors: Yaremchuk, A. / Cusack, S. / Gudzera, O. / Grotli, M. / Tukalo, M.
History
DepositionSep 11, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEUCYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0678
Polymers101,1701
Non-polymers8977
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.410, 155.590, 176.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2499-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LEUCYL-TRNA SYNTHETASE /


Mass: 101170.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ENZYME CONTAINS 878 RESIDUES AND TWO ZINC ATOMS / Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB-27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIE4*PLUS, leucine-tRNA ligase

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Non-polymers , 5 types, 541 molecules

#2: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-LMS / [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE


Type: RNA linking / Mass: 346.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N6O6S
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE C-TERMINAL DOMAIN, RESIDUES 815-878, ARE DISORDERED IN THE CRYSTAL.

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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: 3.5 Å3/Da / Density % sol: 64.4 % / Description: SEE REFERENCE 1
Crystal growpH: 6.5
Details: PROTEIN 10 MG/ML IN 50MM BIS-TRIS PROPANE BUFFER PH 6.0-6.5 2MM DTT, 20MM MGCL2, 1MM NAN3, 18% AMMONIUM SULPHATE EQUILBRIATED AGAINST 30-38% AMMONIUM SULPHATE IN 100MM BIS-TRIS PROPANE ...Details: PROTEIN 10 MG/ML IN 50MM BIS-TRIS PROPANE BUFFER PH 6.0-6.5 2MM DTT, 20MM MGCL2, 1MM NAN3, 18% AMMONIUM SULPHATE EQUILBRIATED AGAINST 30-38% AMMONIUM SULPHATE IN 100MM BIS-TRIS PROPANE BUFFER PH 6.0-6.5. SEE REFERENCE 2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Yaremchuk, A., (2000) Acta Crystallogr.,Sect.D, 56, 667.
PH range low: 6.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMBis-Tris propane1droppH6.0-6.5
32 mMdithiothreitol1drop
420 mM1dropMgCl2
51 mM1dropNaN3
715 %satammonium sulfate1drop
830 %ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 88328 / % possible obs: 90.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.4
Reflection shellResolution: 2→2.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / % possible all: 60.2
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 60.2 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→18.63 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3470650.15 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SIDE-CHAINS ATOMS WITH NO ELECTRON DENSITY HAVE ZERO OCCUPANCY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4402 5 %RANDOM
Rwork0.205 ---
obs0.205 88382 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.8197 Å2 / ksol: 0.357336 e/Å3
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.79 Å20 Å20 Å2
2--8.33 Å20 Å2
3----3.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→18.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 48 534 7224
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.921.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it3.153
X-RAY DIFFRACTIONc_scangle_it4.44
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 538 5.1 %
Rwork0.261 10008 -
obs--67.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. reflection obs: 88980 / % reflection Rfree: 4.6 % / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0065
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11

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