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- PDB-8i2c: E. coli tryptophanyl-tRNA synthetase bound with a chemical fragme... -

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Basic information

Entry
Database: PDB / ID: 8i2c
TitleE. coli tryptophanyl-tRNA synthetase bound with a chemical fragment at the dimerization interface
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / tryptophanyl-tRNA synthetase / dimer interface / fragment screening / antibacterials
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
4-methoxyaniline / TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsXiang, M. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177140 China
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening.
Authors: Xiang, M. / Xia, K. / Chen, B. / Luo, Z. / Yu, Y. / Jiang, L. / Zhou, H.
History
DepositionJan 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan--tRNA ligase
B: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5626
Polymers76,7472
Non-polymers8154
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-40 kcal/mol
Surface area26610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.725, 80.430, 77.136
Angle α, β, γ (deg.)90.00, 106.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 38373.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: trpS, b3384, JW3347 / Production host: Escherichia coli (E. coli) / References: UniProt: P00954, tryptophan-tRNA ligase

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Non-polymers , 5 types, 217 molecules

#2: Chemical ChemComp-O8U / 4-methoxyaniline


Mass: 123.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N7O8P
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.16M Ammonium sulfate, 0. M HEPES pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 44074 / % possible obs: 99.5 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.044 / Rrim(I) all: 0.082 / Net I/σ(I): 13.5
Reflection shellResolution: 2.07→2.13 Å / % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.568 / Num. measured all: 11908 / Num. unique obs: 3433 / CC1/2: 0.841 / Rpim(I) all: 0.356 / Rrim(I) all: 0.672 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V0I

5v0i


Resolution: 2.07→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.498 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23755 2206 5 %RANDOM
Rwork0.20046 ---
obs0.2023 41849 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.952 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å2-0 Å20.79 Å2
2--2.4 Å20 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 2.07→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5035 0 55 213 5303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195201
X-RAY DIFFRACTIONr_bond_other_d0.0020.024703
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9667067
X-RAY DIFFRACTIONr_angle_other_deg0.897310890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2945657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26624.871232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86215836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8051524
X-RAY DIFFRACTIONr_chiral_restr0.0650.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215879
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021024
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_it1.2963.5742637
X-RAY DIFFRACTIONr_mcbond_other1.2953.5752638
X-RAY DIFFRACTIONr_mcangle_it2.0795.3513290
X-RAY DIFFRACTIONr_mcangle_other2.0785.3513291
X-RAY DIFFRACTIONr_scbond_it1.4593.7032564
X-RAY DIFFRACTIONr_scbond_other1.4573.6992561
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3685.4893772
X-RAY DIFFRACTIONr_long_range_B_refined3.75242.4565835
X-RAY DIFFRACTIONr_long_range_B_other3.75242.4615836
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 146 -
Rwork0.267 3084 -
obs--99.48 %

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