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- PDB-7cms: Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus s... -

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Basic information

Entry
Database: PDB / ID: 7cms
TitleCrystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with chuangxinmycin
ComponentsTryptophan--tRNA ligase
KeywordsANTIBIOTIC / Chuangxinmycin
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / 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
Chem-9E0 / PHOSPHATE ION / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLyu, G. / Fan, S. / Jin, Y. / Zou, S. / Wu, G. / Yang, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81761128016 China
National Natural Science Foundation of China (NSFC)81621064 China
Ministry of Science and Technology (MoST, China)2018YFA0901800 China
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural insights into the specific interaction between Geobacillus stearothermophilus tryptophanyl-tRNA synthetase and antimicrobial Chuangxinmycin.
Authors: Fan, S. / Lv, G. / Feng, X. / Wu, G. / Jin, Y. / Yan, M. / Yang, Z.
History
DepositionJul 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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

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)75,1086
Polymers74,4512
Non-polymers6574
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-36 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.675, 91.675, 152.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-728-

HOH

21B-696-

HOH

31B-733-

HOH

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Components

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


Mass: 37225.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: trpS / Production host: Escherichia coli (E. coli) / References: UniProt: P00953, tryptophan-tRNA ligase
#2: Chemical ChemComp-9E0 / (5~{S},6~{R})-5-methyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid


Mass: 233.286 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 1.8M K2HPO4 / PH range: 7.0-7.6

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 37392 / % possible obs: 100 % / Redundancy: 18.6 % / Biso Wilson estimate: 22.55 Å2 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.043 / Rrim(I) all: 0.186 / Χ2: 0.981 / Net I/σ(I): 5.5 / Num. measured all: 871458
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.06-2.114.22.41723500.6550.6552.5050.905100
2.1-2.1316.22.08522910.7550.5242.1510.905100
2.13-2.1717.11.78323080.8280.4371.8360.9100
2.17-2.2218.11.83523030.8350.4381.8870.947100
2.22-2.2718.31.68823110.8470.41.7351.3100
2.27-2.3218.91.30423180.9070.3041.3390.932100
2.32-2.3818.91.08323240.9280.2531.1130.948100
2.38-2.4418.80.91123070.9510.2130.9360.969100
2.44-2.5117.60.80923250.9580.1980.8340.977100
2.51-2.6200.70323260.9730.1590.7210.98100
2.6-2.6920.30.56723320.9790.1270.5810.989100
2.69-2.820.20.4623410.9830.1040.4720.989100
2.8-2.9220.10.36123360.9870.0820.370.998100
2.92-3.0819.70.26823510.9920.0610.2750.999100
3.08-3.2717.90.18723380.9940.0450.1931.043100
3.27-3.5220.10.13923610.9960.0320.1431.066100
3.52-3.8819.90.10723690.9970.0250.1091.044100
3.88-4.4418.90.08723940.9970.0210.091.032100
4.44-5.5918.10.07623940.9960.0190.0790.894100
5.59-5018.10.07425600.9970.0180.0760.77599.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I6M

1i6m


Resolution: 2.2→43.894 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 1629 4.36 %
Rwork0.1694 35763 -
obs0.1712 35763 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.12 Å2 / Biso mean: 27.2486 Å2 / Biso min: 9.65 Å2
Refinement stepCycle: final / Resolution: 2.2→43.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5201 0 42 468 5711
Biso mean--27.37 37.2 -
Num. residues----653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.26480.26231250.2032269691
2.2648-2.33790.2391350.1763286495
2.3379-2.42140.20931290.1665286896
2.4214-2.51840.20361330.1665289096
2.5184-2.6330.21381330.1667294897
2.633-2.77180.20331310.1659300599
2.7718-2.94540.24991370.1787300799
2.9454-3.17270.21251370.16863043100
3.1727-3.49190.22131360.15763049100
3.4919-3.99690.19311440.14793072100
3.9969-5.03450.17091380.14823105100
5.0345-430.21211510.2075321699

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