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- PDB-7ev3: Crystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA... -

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Basic information

Entry
Database: PDB / ID: 7ev3
TitleCrystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA synthetase complexed with Y-10 and ATP
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / TrpRS / aminoacylation / tRNA-binding / aminoacyl-tRNA synthetase / ATP-binding
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / ATP binding / cytoplasm
Similarity search - Function
Tryptophan-tRNA ligase, bacterial-type / : / Tryptophan-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chem-JE3 / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsXu, M. / Chen, S.
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Investigate Natural Product Indolmycin and the Synthetically Improved Analogue Toward Antimycobacterial Agents.
Authors: Yang, Y. / Xu, Y. / Yue, Y. / Wang, H. / Cui, Y. / Pan, M. / Zhang, X. / Zhang, L. / Li, H. / Xu, M. / Tang, Y. / Chen, S.
History
DepositionMay 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1884
Polymers37,3811
Non-polymers8073
Water79344
1
A: Tryptophan--tRNA ligase
hetero molecules

A: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3768
Polymers74,7622
Non-polymers1,6146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_775-y+2,-x+2,-z+1/61
Buried area5950 Å2
ΔGint-56 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.266, 61.266, 333.627
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

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Components

#1: Protein Tryptophan--tRNA ligase / Tryptophanyl-tRNA synthetase / TrpRS


Mass: 37380.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: trpS, DSI38_02915, E5M05_20150, E5M52_19725, E5M78_19780, ERS007657_01660, ERS007661_00440, ERS007663_02313, ERS007665_01484, ERS007670_03000, ERS007679_02115, ERS007681_00969, ERS007688_01638, ...Gene: trpS, DSI38_02915, E5M05_20150, E5M52_19725, E5M78_19780, ERS007657_01660, ERS007661_00440, ERS007663_02313, ERS007665_01484, ERS007670_03000, ERS007679_02115, ERS007681_00969, ERS007688_01638, ERS007703_02455, ERS007722_03290, ERS007741_01346, ERS013471_03442, ERS023446_03614, ERS024276_00235, ERS027659_00823, ERS094182_03915, F6W99_01991, GCL30_20825, SAMEA2683035_03669
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045IZS3, tryptophan-tRNA ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-JE3 / (5S)-5-[(1R)-1-(4-fluoranyl-1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4-one


Mass: 275.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14FN3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 0.2M MgCl2, 35% PEG 400, 0.1M MES, pH 5.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 11213 / % possible obs: 99.8 % / Redundancy: 21.8 % / Biso Wilson estimate: 44.17 Å2 / CC1/2: 0.978 / Net I/σ(I): 15
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 530 / CC1/2: 0.865

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.18.2_3874phasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EL8

7el8


Resolution: 2.7→47.89 Å / SU ML: 0.3056 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6382
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2493 533 4.88 %
Rwork0.2012 10392 -
obs0.2036 10925 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.36 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 52 44 2522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852525
X-RAY DIFFRACTIONf_angle_d1.15143451
X-RAY DIFFRACTIONf_chiral_restr0.0629404
X-RAY DIFFRACTIONf_plane_restr0.0059465
X-RAY DIFFRACTIONf_dihedral_angle_d18.2279923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.970.28471140.25262350X-RAY DIFFRACTION92.32
2.97-3.40.32061430.23312579X-RAY DIFFRACTION99.96
3.4-4.290.2471310.18882610X-RAY DIFFRACTION99.93
4.29-47.890.20851450.18162853X-RAY DIFFRACTION99.97

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