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- PDB-2bte: Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNA... -

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Basic information

Entry
Database: PDB / ID: 2bte
TitleThermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation and a post- transfer editing substrate analogue
Components
  • AMINOACYL-TRNA SYNTHETASE
  • TRNALEU TRANSCRIPT WITH ANTICODON CAG
KeywordsLIGASE / CLASS I AMINOACYL-TRNA SYNTHETASE EDITING
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 / cytosol
Similarity search - Function
Leucyl-tRNA synthetase, domain 3 / Leucyl-tRNA synthetase, domain 3 / Leucyl-tRNA synthetase, domain 3 / Leucine-tRNA synthetase-specific domain / Ubiquitin-like (UB roll) - #590 / 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 ...Leucyl-tRNA synthetase, domain 3 / Leucyl-tRNA synthetase, domain 3 / Leucyl-tRNA synthetase, domain 3 / Leucine-tRNA synthetase-specific domain / Ubiquitin-like (UB roll) - #590 / 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 / Ubiquitin-like (UB roll) / Roll / Roll / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-AMINO-2'-DEOXYADENOSINE / : / LEUCINE / NORVALINE / RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsCusack, S. / Tukalo, M. / Yaremchuk, A. / Fukunaga, R. / Yokoyama, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The Crystal Structure of Leucyl-tRNA Synthetase Complexed with tRNA(Leu) in the Post-Transfer- Editing Conformation.
Authors: Tukalo, M. / Yaremchuk, A. / Fukunaga, R. / Yokoyama, S. / Cusack, S.
History
DepositionMay 31, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AMINOACYL-TRNA SYNTHETASE
B: TRNALEU TRANSCRIPT WITH ANTICODON CAG
D: AMINOACYL-TRNA SYNTHETASE
E: TRNALEU TRANSCRIPT WITH ANTICODON CAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,23041
Polymers256,1364
Non-polymers4,09437
Water32418
1
A: AMINOACYL-TRNA SYNTHETASE
B: TRNALEU TRANSCRIPT WITH ANTICODON CAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,06720
Polymers128,0682
Non-polymers1,99918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-203.4 kcal/mol
Surface area48940 Å2
MethodPISA
2
D: AMINOACYL-TRNA SYNTHETASE
E: TRNALEU TRANSCRIPT WITH ANTICODON CAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,16321
Polymers128,0682
Non-polymers2,09519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-205 kcal/mol
Surface area48820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.121, 125.705, 175.432
Angle α, β, γ (deg.)90.00, 120.86, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.47528, -0.010048, 0.879777), (0.003033, -0.99991, -0.013058), (0.879829, 0.008875, -0.475207)
Vector: -17.702, 46.683, 30.1918)

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Components

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Protein / RNA chain , 2 types, 4 molecules ADBE

#1: Protein AMINOACYL-TRNA SYNTHETASE / LEUCYL-TRNA SYNTHETASE


Mass: 101170.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIE4, leucine-tRNA ligase
#2: RNA chain TRNALEU TRANSCRIPT WITH ANTICODON CAG


Mass: 26898.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) THERMUS THERMOPHILUS (bacteria)

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Non-polymers , 7 types, 55 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NVA / NORVALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2
#7: Chemical ChemComp-2AD / 2'-AMINO-2'-DEOXYADENOSINE


Type: L-peptide linking / Mass: 266.257 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N6O3
#8: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsATP + L-LEUCINE + TRNA (LEU) GIVES AMP + PPI L-LEUCYL-TRNA(LEU)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68 %
Crystal growpH: 6.5
Details: 5MG/ML LEUCYL-TRNA SYNTHETASE MOLAR RATIO PROTEIN:TRNA 1.0:1.2 5 MM L-LEUCINE 15MM MGCL2 50MM MES PH6.5 0.8M AMMONIUM SULPHATE AGAINST RESERVOIR CONTAINING 1.5M AMMONIUM SULPHATE AND 0.1M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 6, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 79012 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 5.55 % / Biso Wilson estimate: 83.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.53
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.36 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.14 / % possible all: 51.2

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H3N

1h3n


Resolution: 2.9→24.89 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 784253010.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2369 3 %RANDOM
Rwork0.217 ---
obs0.217 78938 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.5564 Å2 / ksol: 0.320978 e/Å3
Displacement parametersBiso mean: 82.2 Å2
Baniso -1Baniso -2Baniso -3
1-19.74 Å20 Å233.88 Å2
2---16.1 Å20 Å2
3----3.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.78 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 2.9→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14244 3352 201 18 17815
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it4.533
X-RAY DIFFRACTIONc_scangle_it7.24
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.478 270 3 %
Rwork0.478 8722 -
obs--64.1 %
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.PARAM

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