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

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Basic information

Entry
Database: PDB / ID: 7elt
TitleCrystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA synthetase complexed with Trp-AMP
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 / cytosol
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
TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionApr 12, 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)37,9142
Polymers37,3811
Non-polymers5331
Water5,891327
1
A: Tryptophan--tRNA ligase
hetero molecules

A: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8294
Polymers74,7622
Non-polymers1,0672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_775-y+2,-x+2,-z+1/61
Buried area6330 Å2
ΔGint-39 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.405, 61.405, 334.947
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-546-

HOH

21A-615-

HOH

31A-682-

HOH

41A-811-

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 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A045IZS3, tryptophan-tRNA ligase
#2: Chemical ChemComp-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N7O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.51 Å3/Da / Density % sol: 51 %
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: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 30917 / % possible obs: 99.6 % / Redundancy: 15.6 % / Biso Wilson estimate: 21.71 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.139 / Net I/σ(I): 24.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 16.4 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1486 / CC1/2: 0.967 / CC star: 0.992 / % possible all: 98.5

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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: 1.9→48.01 Å / SU ML: 0.1885 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.9403
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2326 1545 5.01 %
Rwork0.1953 29263 -
obs0.1971 30808 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.33 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 37 327 2880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892603
X-RAY DIFFRACTIONf_angle_d1.06673550
X-RAY DIFFRACTIONf_chiral_restr0.0676413
X-RAY DIFFRACTIONf_plane_restr0.0056464
X-RAY DIFFRACTIONf_dihedral_angle_d15.3605945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.26281270.24352551X-RAY DIFFRACTION98.86
1.96-2.030.26071260.21952607X-RAY DIFFRACTION99.71
2.03-2.110.26591380.21052605X-RAY DIFFRACTION99.78
2.11-2.210.2771400.21042582X-RAY DIFFRACTION99.93
2.21-2.330.23551360.20612617X-RAY DIFFRACTION99.96
2.33-2.470.22831430.20272634X-RAY DIFFRACTION99.86
2.47-2.660.26091290.20272668X-RAY DIFFRACTION99.96
2.66-2.930.25391370.2062646X-RAY DIFFRACTION99.89
2.93-3.350.25871580.19532668X-RAY DIFFRACTION99.93
3.35-4.220.1891330.16922742X-RAY DIFFRACTION99.45
4.23-48.010.20841780.18522943X-RAY DIFFRACTION99.11

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