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- PDB-8i1z: E. coli tryptophanyl-tRNA synthetase bound with a chemical fragment -

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Basic information

Entry
Database: PDB / ID: 8i1z
TitleE. coli tryptophanyl-tRNA synthetase bound with a chemical fragment
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-(2,3-dihydro-1-benzofuran-5-yl)ethanone / TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 13, 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)77,7317
Polymers76,7472
Non-polymers9845
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-75 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.790, 80.150, 78.700
Angle α, β, γ (deg.)90.00, 105.77, 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-O7R / 1-(2,3-dihydro-1-benzofuran-5-yl)ethanone


Mass: 162.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50.01 Å / Num. obs: 67909 / % possible obs: 99.2 % / Redundancy: 3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.035 / Rrim(I) all: 0.064 / Χ2: 0.89 / Net I/σ(I): 11.6 / Num. measured all: 204490
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 98.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.374 / Num. measured all: 9006 / Num. unique obs: 4029 / CC1/2: 0.88 / Rpim(I) all: 0.306 / Rrim(I) all: 0.485 / Χ2: 0.78 / Net I/σ(I) obs: 2.2

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Processing

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

5v0i


Resolution: 1.8→50.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.397 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22855 3454 5.1 %RANDOM
Rwork0.19501 ---
obs0.19669 64433 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.245 Å2
Baniso -1Baniso -2Baniso -3
1--2.84 Å20 Å20.64 Å2
2--3.4 Å20 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 1.8→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5109 0 64 361 5534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195275
X-RAY DIFFRACTIONr_bond_other_d0.0010.024824
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9677154
X-RAY DIFFRACTIONr_angle_other_deg0.88311185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2315657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6824.726237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6815885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5731527
X-RAY DIFFRACTIONr_chiral_restr0.0630.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021033
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_it1.1623.4232638
X-RAY DIFFRACTIONr_mcbond_other1.1623.4232639
X-RAY DIFFRACTIONr_mcangle_it1.8795.1273292
X-RAY DIFFRACTIONr_mcangle_other1.8765.1273291
X-RAY DIFFRACTIONr_scbond_it1.3873.6022637
X-RAY DIFFRACTIONr_scbond_other1.3873.5912626
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3285.3073845
X-RAY DIFFRACTIONr_long_range_B_refined3.65840.8845949
X-RAY DIFFRACTIONr_long_range_B_other3.5840.595863
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 269 -
Rwork0.297 4730 -
obs--98.68 %

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