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- PDB-7el8: Crystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA... -

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Basic information

Entry
Database: PDB / ID: 7el8
TitleCrystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA synthetase
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / aminoacylation / tRNA-binding / aminoacyl-tRNA synthetase / ATP-binding
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / 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
Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 9, 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


Theoretical massNumber of molelcules
Total (without water)37,3811
Polymers37,3811
Non-polymers00
Water3,711206
1
A: Tryptophan--tRNA ligase

A: Tryptophan--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)74,7622
Polymers74,7622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_775-y+2,-x+2,-z+1/61
Buried area4050 Å2
ΔGint-35 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.683, 61.683, 334.105
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-433-

HOH

21A-487-

HOH

31A-527-

HOH

41A-537-

HOH

51A-574-

HOH

61A-600-

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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.32 %
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: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23425 / % possible obs: 100 % / Redundancy: 36.6 % / Biso Wilson estimate: 25.46 Å2 / CC1/2: 0.912 / CC star: 0.977 / Rmerge(I) obs: 0.129 / Net I/σ(I): 5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 38.3 % / Rmerge(I) obs: 0.964 / Mean I/σ(I) obs: 6.75 / Num. unique obs: 1133 / CC1/2: 0.975 / CC star: 0.994 / % possible all: 100

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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: 5DK4

5dk4


Resolution: 2.1→48.16 Å / SU ML: 0.2114 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7527
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2437 1138 4.94 %
Rwork0.2147 21914 -
obs0.2162 23052 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 0 206 2614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872452
X-RAY DIFFRACTIONf_angle_d0.97653342
X-RAY DIFFRACTIONf_chiral_restr0.0567394
X-RAY DIFFRACTIONf_plane_restr0.0059440
X-RAY DIFFRACTIONf_dihedral_angle_d19.0318887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.20.29661250.2492631X-RAY DIFFRACTION97.8
2.2-2.310.31751430.2492651X-RAY DIFFRACTION99.61
2.31-2.460.30271620.23982672X-RAY DIFFRACTION99.61
2.46-2.650.27191190.22332719X-RAY DIFFRACTION99.47
2.65-2.910.24991320.23162720X-RAY DIFFRACTION99.06
2.91-3.330.23571500.22112711X-RAY DIFFRACTION98.21
3.33-4.20.22211510.18542771X-RAY DIFFRACTION98.45
4.2-48.160.20831560.20333039X-RAY DIFFRACTION99.38

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