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- PDB-5ah5: Crystal structure of the ternary complex of Agrobacterium radioba... -

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Basic information

Entry
Database: PDB / ID: 5ah5
TitleCrystal structure of the ternary complex of Agrobacterium radiobacter K84 agnB2 LeuRS-tRNA-LeuAMS
Components
  • LEUCINE--TRNA LIGASE
  • TRNA-LEU TAA ISOACCEPTOR
KeywordsLIGASE/RNA / LIGASE-RNA COMPLEX / LEUCINE-TRNA / LEUCINE-TRNA LIGASE ACTIVITY ATP + L-LEUCINE + TRNA(LEU) GIVES AMP + DIPHOSPHATE + L-LEUCYL-TRNA(LEU) / AMINOACYL- TRNA EDITING ACTIVITY / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS / TOXIC MOEITY 84 RESISTANCE
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 / cytoplasm
Similarity search - Function
Ubiquitin-like (UB roll) - #590 / Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / 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 ...Ubiquitin-like (UB roll) - #590 / Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / 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. / Rossmann-like alpha/beta/alpha sandwich fold / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
5'-O-(L-leucylsulfamoyl)adenosine / : / RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesAGROBACTERIUM RADIOBACTER K84 (bacteria)
AGROBACTERIUM TUMEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPalencia, A. / Chopra, S. / Virus, C. / Schulwitz, S. / Temple, B.R. / Cusack, S. / Reader, J.S.
CitationJournal: Nat.Commun. / Year: 2016
Title: Structural Characterization of Antibiotic Self-Immunity tRNA Synthetase in Plant Tumour Biocontrol Agent.
Authors: Chopra, S. / Palencia, A. / Virus, C. / Schulwitz, S. / Temple, B.R. / Cusack, S. / Reader, J.
History
DepositionFeb 5, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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: LEUCINE--TRNA LIGASE
C: TRNA-LEU TAA ISOACCEPTOR
D: TRNA-LEU TAA ISOACCEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,26115
Polymers238,6214
Non-polymers1,64011
Water15,691871
1
B: LEUCINE--TRNA LIGASE
D: TRNA-LEU TAA ISOACCEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1798
Polymers119,3112
Non-polymers8686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-75.3 kcal/mol
Surface area43960 Å2
MethodPISA
2
A: LEUCINE--TRNA LIGASE
C: TRNA-LEU TAA ISOACCEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,0837
Polymers119,3112
Non-polymers7725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-62.3 kcal/mol
Surface area44360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.910, 50.320, 170.520
Angle α, β, γ (deg.)90.00, 93.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

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


Mass: 92351.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AGROBACTERIUM RADIOBACTER K84 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: B9JQP8, leucine-tRNA ligase
#2: RNA chain TRNA-LEU TAA ISOACCEPTOR


Mass: 26959.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AGROBACTERIUM TUMEFACIENS (bacteria) / Strain: C58 / Production host: ESCHERICHIA COLI K-12 (bacteria)

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Non-polymers , 5 types, 882 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-LSS / 5'-O-(L-leucylsulfamoyl)adenosine / 5-O-N-LEUCYL-SULFAMOYLADENOSINE


Mass: 459.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N7O7S
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 871 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCONTAINS A C-TERM TAG BELONGING TO THE EXPRESSION VECTOR PET28-A

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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: 2.9 Å3/Da / Density % sol: 58.5 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M MES PH 6.5, 0.2 M AMMONIUM SULFATE, 27 % PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97934
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→48.6 Å / Num. obs: 160330 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2BTE, 4AS1

2bte

4as1


Resolution: 2.1→48.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.191 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23732 8487 5 %RANDOM
Rwork0.19416 ---
obs0.19634 160330 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.507 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0.79 Å2
2--0 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12364 3423 91 871 16749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01716645
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213607
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.78923394
X-RAY DIFFRACTIONr_angle_other_deg1.137331481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.70551570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3523.389602
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.711152110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.68715106
X-RAY DIFFRACTIONr_chiral_restr0.1120.22563
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02116397
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023886
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_it4.0584.8486268
X-RAY DIFFRACTIONr_mcbond_other4.0584.8486268
X-RAY DIFFRACTIONr_mcangle_it5.7987.2397827
X-RAY DIFFRACTIONr_mcangle_other5.7987.2387828
X-RAY DIFFRACTIONr_scbond_it4.6635.30810377
X-RAY DIFFRACTIONr_scbond_other4.6445.30110358
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0057.8615533
X-RAY DIFFRACTIONr_long_range_B_refined9.17941.54920232
X-RAY DIFFRACTIONr_long_range_B_other9.16441.54119955
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 635 -
Rwork0.309 11686 -
obs--99.67 %

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