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- PDB-8i2j: E. coli tryptophanyl-tRNA synthetase bound with a chemical fragme... -

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Basic information

Entry
Database: PDB / ID: 8i2j
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
1-(4-methoxyphenyl)ethanone / TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 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)77,5275
Polymers76,7472
Non-polymers7803
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-51 kcal/mol
Surface area26590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.795, 80.423, 78.658
Angle α, β, γ (deg.)90.00, 105.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-O9F / 1-(4-methoxyphenyl)ethanone


Mass: 150.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N7O8P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.16M Ammonium sulfate, 0.1M HEPES pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 21631 / % possible obs: 99.7 % / Redundancy: 4 % / CC1/2: 0.984 / Rpim(I) all: 0.079 / Rrim(I) all: 0.164 / Net I/σ(I): 9.6
Reflection shellResolution: 2.65→2.79 Å / % possible obs: 100 % / Redundancy: 4.1 % / Num. measured all: 13122 / Num. unique obs: 3166 / CC1/2: 0.853 / Rpim(I) all: 0.225 / Rrim(I) all: 0.467 / Net I/σ(I) obs: 3.6

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Processing

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

5v0i


Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.856 / SU B: 12.189 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 30.706 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26021 1100 5.1 %RANDOM
Rwork0.22449 ---
obs0.22624 20518 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.645 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0 Å20.4 Å2
2--1.75 Å20 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5004 0 53 72 5129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195158
X-RAY DIFFRACTIONr_bond_other_d0.0010.024688
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.9687006
X-RAY DIFFRACTIONr_angle_other_deg0.851310843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1155650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26424.714227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64615833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2591525
X-RAY DIFFRACTIONr_chiral_restr0.0530.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215811
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021017
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_it0.3422.2842615
X-RAY DIFFRACTIONr_mcbond_other0.3422.2832616
X-RAY DIFFRACTIONr_mcangle_it0.6453.4233259
X-RAY DIFFRACTIONr_mcangle_other0.6453.4233260
X-RAY DIFFRACTIONr_scbond_it0.1722.2482543
X-RAY DIFFRACTIONr_scbond_other0.1722.2462540
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3553.3613742
X-RAY DIFFRACTIONr_long_range_B_refined1.36626.4265617
X-RAY DIFFRACTIONr_long_range_B_other1.36526.435616
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 84 -
Rwork0.302 1503 -
obs--99.87 %

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