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- PDB-4aq7: Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and ... -

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Basic information

Entry
Database: PDB / ID: 4aq7
TitleTernary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and leucyl-adenylate analogue in the aminoacylation conformation
Components
  • E. COLI TRNALEU UAA ISOACCEPTOR
  • LEUCINE--TRNA LIGASE
KeywordsLIGASE/RNA / LIGASE-RNA COMPLEX / LIGASE / NUCLEOTIDE(ATP)-BINDING / PROTEIN BIOSYNTHESIS / CLASS I AMINOACYL-TRNA SYNTHETASE / ATP-BINDING / METAL-BINDING
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing 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 / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia ...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 / 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 / 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
LEUCINE / Chem-LMS / RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPalencia, A. / Crepin, T. / Vu, M.T. / Lincecum Jr, T.L. / Martinis, S.A. / Cusack, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural Dynamics of the Aminoacylation and Proofreading Functional Cycle of Bacterial Leucyl-tRNA Synthetase
Authors: Palencia, A. / Crepin, T. / Vu, M.T. / Lincecum Jr, T.L. / Martinis, S.A. / Cusack, S.
History
DepositionApr 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Other
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Oct 31, 2012Group: Atomic model
Revision 1.4Dec 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_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.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 / _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: LEUCINE--TRNA LIGASE
B: E. COLI TRNALEU UAA ISOACCEPTOR
D: LEUCINE--TRNA LIGASE
E: E. COLI TRNALEU UAA ISOACCEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,27212
Polymers255,1374
Non-polymers1,1348
Water3,045169
1
A: LEUCINE--TRNA LIGASE
B: E. COLI TRNALEU UAA ISOACCEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,1366
Polymers127,5692
Non-polymers5674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-61.4 kcal/mol
Surface area47170 Å2
MethodPISA
2
D: LEUCINE--TRNA LIGASE
E: E. COLI TRNALEU UAA ISOACCEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,1366
Polymers127,5692
Non-polymers5674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-95.2 kcal/mol
Surface area47850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.660, 69.200, 228.840
Angle α, β, γ (deg.)90.00, 104.35, 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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P07813, leucine-tRNA ligase
#2: RNA chain E. COLI TRNALEU UAA ISOACCEPTOR


Mass: 28052.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)

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Non-polymers , 5 types, 177 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: 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.: 2 / Source method: obtained synthetically / Formula: C10H14N6O6S
#5: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsATP + L-LEUCINE + TRNA (GIVES AMP + PPI + L-LEUCYL-TRNA(LEU)
Nonpolymer details[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3, 4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE (LMS): ...[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3, 4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE (LMS): SUPHAMOYL ANALOGUES OF LEUCYL-ADENYLATE

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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: 1.9 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 5.5
Details: 33 MICROM LEURS, 50 MICROM TRNALEU AND 1 MM LEUCYL-ADENYLATE ANALOGUE MIXED EQUALLY WITH 0.1 M BIS-TRIS PH 5.5, 23-25% W/V PEG 3350, AND 200 MM AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9375
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9375 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 75711 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.16 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.1 / % possible all: 76.6

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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 1H3N

1h3n


Resolution: 2.5→39.69 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / SU B: 23.548 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 1.175 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25031 3826 5.1 %RANDOM
Rwork0.18752 ---
obs0.19075 71885 90.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.175 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.07 Å2
2---0.62 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13670 3307 66 169 17212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01817748
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210964
X-RAY DIFFRACTIONr_angle_refined_deg1.771.84224843
X-RAY DIFFRACTIONr_angle_other_deg1.086326700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28251718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96624.551668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.305152382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3811582
X-RAY DIFFRACTIONr_chiral_restr0.0940.22688
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02117531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023696
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 246 -
Rwork0.353 4344 -
obs--75.86 %
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)
12.69121.6209-0.41531.9468-0.75771.23110.1198-0.02430.10520.2506-0.03410.0278-0.0320.0379-0.08570.0452-0.0019-0.01010.0152-0.01470.0244-28.14891.3143-77.6752
22.04370.36930.65281.73310.0131.3606-0.06820.01760.14080.07490.05010.53820.0477-0.39320.01810.0561-0.01230.04070.14380.00320.2703-58.05679.063-86.2009
31.5941-0.0590.58732.95540.93772.2253-0.1077-0.06910.22050.3273-0.01710.1346-0.15580.11640.12480.1716-0.064-0.03650.27090.02990.266-24.954635.7206-108.6944
410.3139-5.87744.11386.1613-2.88556.27290.36270.3503-0.4029-0.4728-0.13240.32170.6529-0.2626-0.23030.1303-0.1223-0.08150.24680.02540.2512-72.9683-8.8897-100.431
54.8947-3.8958-0.908312.61191.77714.2536-0.3991-0.47950.79830.4460.41510.4703-0.5766-0.4027-0.0160.31990.06320.02230.1468-0.07190.3375-42.459624.5915-68.7251
63.04850.88510.47691.0294-0.18741.5812-0.14340.1660.0202-0.15860.08810.04290.08840.02590.05530.3564-0.0415-0.03710.13960.00650.0333-55.661539.7216-37.9388
75.35680.87160.67241.40370.18251.2262-0.0934-0.4121-0.7977-0.02580.02670.13580.3244-0.34290.06670.5127-0.04420.05110.34020.02390.2884-70.111213.5814-28.3939
82.2418-0.4428-0.77743.4455-0.79473.32640.05490.28110.143-0.4384-0.1139-0.61290.10080.30790.0590.39860.0461-0.01180.4360.07410.2548-28.45420.9925-4.7844
93.9147-0.09550.41537.8321-2.74345.08740.0893-0.7464-0.34820.56750.12960.9328-0.031-0.5207-0.21890.4306-0.083-0.06660.87360.15790.5321-94.199115.9019-14.3124
104.9145-6.9541-3.147610.1655.95749.3425-0.04930.2003-0.3590.2736-0.1810.43550.91090.33590.23030.4044-0.00820.06890.3314-0.08060.402-48.826112.8212-46.0128
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 DIFFRACTION1A901
5X-RAY DIFFRACTION1B84 - 87
6X-RAY DIFFRACTION2B1 - 76
7X-RAY DIFFRACTION3A231 - 415
8X-RAY DIFFRACTION4A795 - 860
9X-RAY DIFFRACTION5A569 - 628
10X-RAY DIFFRACTION6D1 - 230
11X-RAY DIFFRACTION6D416 - 568
12X-RAY DIFFRACTION6D629 - 794
13X-RAY DIFFRACTION6D901
14X-RAY DIFFRACTION6E84 - 87
15X-RAY DIFFRACTION7E1 - 76
16X-RAY DIFFRACTION8D231 - 415
17X-RAY DIFFRACTION9D795 - 860
18X-RAY DIFFRACTION10D569 - 628

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