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- PDB-2v0c: LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A... -

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Basic information

Entry
Database: PDB / ID: 2v0c
TitleLEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A SULPHAMOYL ANALOGUE OF LEUCYL-ADENYLATE In the synthetic site and an adduct of AMP with 5-Fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (AN2690) in the editing site
ComponentsAMINOACYL-TRNA SYNTHETASE
KeywordsLIGASE / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / CLSS I AMINOACYL- TRNA SYNTHETASE / ATP + L-LEUCINE + TRNA (LEU) GIVES AMP + PPI + L-LEUCYL-TRNA(LEU) / AMINOACYL-TRNA SYNTHETASE / ZINC / ATP-BINDING / METAL-BINDING
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase 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 / 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 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Isoleucyl-tRNA Synthetase; Domain 1 / 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
Chem-ANZ / LEUCINE / Chem-LMS / Leucine--tRNA ligase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRock, F. / Mao, W. / Yaremchuk, A. / Tukalo, M. / Crepin, T. / Zhou, H. / Zhang, Y. / Hernandez, V. / Akama, T. / Baker, S. ...Rock, F. / Mao, W. / Yaremchuk, A. / Tukalo, M. / Crepin, T. / Zhou, H. / Zhang, Y. / Hernandez, V. / Akama, T. / Baker, S. / Plattner, J. / Shapiro, L. / Martinis, S.A. / Benkovic, S.J. / Cusack, S. / Alley, M.R.K.
CitationJournal: Science / Year: 2007
Title: An Antifungal Agent Inhibits an Aminoacyl-tRNA Synthetase by Trapping tRNA in the Editing Site.
Authors: Rock, F. / Mao, W. / Yaremchuk, A. / Tukalo, M. / Crepin, T. / Zhou, H. / Zhang, Y. / Hernandez, V. / Akama, T. / Baker, S. / Plattner, J. / Shapiro, L. / Martinis, S.A. / Benkovic, S.J. / ...Authors: Rock, F. / Mao, W. / Yaremchuk, A. / Tukalo, M. / Crepin, T. / Zhou, H. / Zhang, Y. / Hernandez, V. / Akama, T. / Baker, S. / Plattner, J. / Shapiro, L. / Martinis, S.A. / Benkovic, S.J. / Cusack, S. / Alley, M.R.K.
History
DepositionMay 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_asym_id / _struct_conn.ptnr1_label_atom_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
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: AMINOACYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,56711
Polymers100,9981
Non-polymers1,56910
Water12,322684
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.830, 154.230, 174.950
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-2643-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 100997.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB-27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIE4

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Non-polymers , 6 types, 694 molecules

#2: Chemical ChemComp-LEU / 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-ANZ / [(6-AMINO-9H-PURIN-9-YL)-[5-FLUORO-1,3-DIHYDRO-1-HYDROXY-2,1-BENZOXABOROLE]-4'YL]METHYL DIHYDROGEN PHOSPHATE


Mass: 480.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17BFN5O8P
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 3.5 Å3/Da / Density % sol: 64.4 %
Crystal growDetails: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 472672 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.86
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.42 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H3N

1h3n


Resolution: 1.85→87.37 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.236 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. C-TERMINAL DOMAIN RESIDUES 814-878 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3477 3 %RANDOM
Rwork0.18 ---
obs0.181 112717 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.85 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.85→87.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6608 0 91 684 7383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226895
X-RAY DIFFRACTIONr_bond_other_d0.0010.024826
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9759373
X-RAY DIFFRACTIONr_angle_other_deg0.94311661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.15223.233331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.839151149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.741555
X-RAY DIFFRACTIONr_chiral_restr0.1060.2963
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021463
X-RAY DIFFRACTIONr_nbd_refined0.2110.21335
X-RAY DIFFRACTIONr_nbd_other0.1970.25056
X-RAY DIFFRACTIONr_nbtor_refined0.1810.23221
X-RAY DIFFRACTIONr_nbtor_other0.0850.23356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2521
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.340.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2951.55251
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37526533
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.34133464
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3694.52840
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 240
Rwork0.254 7744

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