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- PDB-3zgz: Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and ... -

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Basic information

Entry
Database: PDB / ID: 3zgz
TitleTernary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and toxic moiety from agrocin 84 (TM84) in aminoacylation-like conformation
Components
  • LEUCINE--TRNA LIGASE
  • TRNA-LEU UAA ISOACCEPTOR
KeywordsLIGASE/RNA / LIGASE-RNA COMPLEX / LIGASE / NUCLEOTIDE(ATP)-BINDING / PROTEIN BIOSYNTHESIS / CLASS I AMINOACYL-TRNA SYNTHETASE
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / ATP binding / cytosol
Similarity search - Function
Rubrerythrin, domain 2 - #290 / 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 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) ...Rubrerythrin, domain 2 - #290 / 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 / 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 / Rubrerythrin, domain 2 / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Single Sheet / Rossmann-like alpha/beta/alpha sandwich fold / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-84T / RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
ESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChopra, S. / Palencia, A. / Virus, C. / Tripathy, A. / Temple, B.R. / Velazquez-Campoy, A. / Cusack, S. / Reader, J.S.
CitationJournal: Nat.Commun. / Year: 2013
Title: Plant Tumour Biocontrol Agent Employs a tRNA-Dependent Mechanism to Inhibit Leucyl-tRNA Synthetase
Authors: Chopra, S. / Palencia, A. / Virus, C. / Tripathy, A. / Temple, B.R. / Velazquez-Campoy, A. / Cusack, S. / Reader, J.S.
History
DepositionDec 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Dec 20, 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_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_asym_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_asym_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.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 / _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: LEUCINE--TRNA LIGASE
B: TRNA-LEU UAA ISOACCEPTOR
D: LEUCINE--TRNA LIGASE
E: TRNA-LEU UAA ISOACCEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,04715
Polymers255,8264
Non-polymers1,22211
Water6,648369
1
A: LEUCINE--TRNA LIGASE
B: TRNA-LEU UAA ISOACCEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5609
Polymers127,9132
Non-polymers6477
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-81.4 kcal/mol
Surface area46080 Å2
MethodPISA
2
D: LEUCINE--TRNA LIGASE
E: TRNA-LEU UAA ISOACCEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4876
Polymers127,9132
Non-polymers5744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-68.7 kcal/mol
Surface area48280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.580, 68.190, 226.220
Angle α, β, γ (deg.)90.00, 105.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / RNA chain , 2 types, 4 molecules ADBE

#1: Protein LEUCINE--TRNA LIGASE / LEUCYL-TRNA SYNTHETASE / LEURS


Mass: 99516.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P07813, leucine-tRNA ligase
#2: RNA chain TRNA-LEU UAA ISOACCEPTOR


Mass: 28396.875 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI K-12 (bacteria)

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Non-polymers , 4 types, 380 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-84T / [(2S,4S,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methoxy-N-[(2S,3R)-4-methyl-2,3-bis(oxidanyl)pentanoyl]phosphonamidic acid


Mass: 460.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N6O8P
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTOXIC MOIETY FROM AGROCIN 84 (TM84) (84T): TM84 WAS PURIFIED FROM CELLULAR CULTURES OF ...TOXIC MOIETY FROM AGROCIN 84 (TM84) (84T): TM84 WAS PURIFIED FROM CELLULAR CULTURES OF AGROBACTERIUM RADIOBACTER K84 STRAIN

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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: 2.29 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 5.5 / Details: 0.1 M BIS-TRIS, 23-25 % PEG 3350, PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 85255 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 3.91 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.2
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.8 / % possible all: 65.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AQ7

4aq7


Resolution: 2.4→43.59 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 16.952 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.593 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23822 4280 5 %RANDOM
Rwork0.18681 ---
obs0.18941 80975 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.815 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.75 Å2
2--0.26 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13715 3367 71 369 17522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01817878
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211029
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.84225039
X-RAY DIFFRACTIONr_angle_other_deg0.987326847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67351724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7724.544669
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.236152387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9961582
X-RAY DIFFRACTIONr_chiral_restr0.0780.22705
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117601
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023721
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 180 -
Rwork0.343 3586 -
obs--56.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.09951.1065-0.4261.3254-0.52620.7868-0.0008-0.08850.05940.1140.0012-0.0206-0.05390.0269-0.00040.11370.00760.01710.00970.00180.0558-26.82581.7587-76.5306
22.39050.25860.79092.02240.07311.1271-0.1216-0.05320.11280.01360.09160.48510.0145-0.30730.030.0937-0.0082-0.00810.10290.01930.2874-58.63338.8155-85.1066
31.601-0.6475-0.19873.22290.81371.5641-0.0368-0.26070.06850.4657-0.08990.0820.08330.05650.12680.2341-0.03150.01580.15160.03060.2123-23.405635.9351-107.2324
43.8125-3.11270.11214.4419-0.20422.33150.05960.273-0.0705-0.14820.00620.15040.2868-0.0275-0.06580.1697-0.1015-0.03110.18150.05590.3117-71.5757-8.5748-98.9813
55.3185-1.5769-2.01959.8021.79663.6772-0.3697-0.43550.82870.3290.34340.185-0.44490.02470.02630.32860.0796-0.02240.0772-0.05960.2329-40.529924.6289-67.915
63.33571.20320.21661.2154-0.1731.5748-0.0179-0.19570.0262-0.0771-0.00810.0415-0.00780.03470.0260.37330.1585-0.00770.3391-0.02190.1336-55.306238.5102-37.2534
74.83810.6296-0.04461.2436-0.18691.07270.0566-0.6796-0.84580.024-0.09490.09520.4304-0.27450.03830.55340.0561-0.01820.60140.12250.4984-71.803611.1189-27.4708
81.4113-0.41070.77752.57840.99833.99160.4692-0.0351-0.1804-0.269-0.5064-0.66320.17390.1610.03720.8386-0.0393-0.13281.17380.2530.6443-28.662119.9655-4.3208
93.16351.8482-2.093810.8532-3.35033.3750.2081-1.0718-0.17490.80290.08320.4354-0.2737-0.2905-0.29120.5125-0.0327-0.13521.36350.09820.4621-93.807614.5495-14.1034
105.0336-6.5707-1.964410.04665.00458.1113-0.3849-0.2447-0.48340.45630.37040.06940.63740.10840.01440.39490.03550.12270.34420.0240.4559-47.762712.3745-44.9678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 230
2X-RAY DIFFRACTION1A416 - 568
3X-RAY DIFFRACTION1A629 - 794
4X-RAY DIFFRACTION1A1862
5X-RAY DIFFRACTION1B84 - 87
6X-RAY DIFFRACTION2B1 - 83
7X-RAY DIFFRACTION3A231 - 415
8X-RAY DIFFRACTION4A795 - 860
9X-RAY DIFFRACTION5A569 - 628
10X-RAY DIFFRACTION6D-8 - 230
11X-RAY DIFFRACTION6D416 - 568
12X-RAY DIFFRACTION6D629 - 794
13X-RAY DIFFRACTION6D1862
14X-RAY DIFFRACTION6E84 - 87
15X-RAY DIFFRACTION7E1 - 83
16X-RAY DIFFRACTION8D231 - 415
17X-RAY DIFFRACTION9D795 - 860
18X-RAY DIFFRACTION10D569 - 628

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