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- PDB-5dk4: Crystal structure analysis of Tryptophanyl-trna synthetase from B... -

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Basic information

Entry
Database: PDB / ID: 5dk4
TitleCrystal structure analysis of Tryptophanyl-trna synthetase from Bacillus stearothermophilus in complex with indolmycin and Mg*ATP
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE/LIGASE INHIBITOR / aaRS / inhibitor / LIGASE-LIGASE INHIBITOR complex
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 / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / 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. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...Tryptophan-tRNA ligase, bacterial-type / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / 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. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-5BX / ADENOSINE-5'-TRIPHOSPHATE / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWilliams, T. / Yin, W.Y. / Carter Jr., C.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM40906 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Selective Inhibition of Bacterial Tryptophanyl-tRNA Synthetases by Indolmycin Is Mechanism-based.
Authors: Williams, T.L. / Yin, Y.W. / Carter, C.W.
History
DepositionSep 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6335
Polymers37,7521
Non-polymers8814
Water4,504250
1
A: Tryptophan--tRNA ligase
hetero molecules

A: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,26510
Polymers75,5032
Non-polymers1,7628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6770 Å2
ΔGint-41 kcal/mol
Surface area26720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.041, 62.041, 219.058
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 37751.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: trpS / Plasmid: pet28 / Production host: Escherichia coli (E. coli) / References: UniProt: P00953, tryptophan-tRNA ligase

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Non-polymers , 5 types, 254 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-5BX / (5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4(5H)-one / Indolemycin, Indolmycin


Mass: 257.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: hepes, potassium citrate, magnesium chloride / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97949 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979491
ReflectionResolution: 1.9→31.02 Å / Num. obs: 34849 / % possible obs: 100 % / Redundancy: 15 % / Net I/σ(I): 10.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→31.02 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.53 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1889 3224 5.01 %
Rwork0.1692 --
obs0.1702 64339 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 57 250 2912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052744
X-RAY DIFFRACTIONf_angle_d0.9943729
X-RAY DIFFRACTIONf_dihedral_angle_d17.1891062
X-RAY DIFFRACTIONf_chiral_restr0.07411
X-RAY DIFFRACTIONf_plane_restr0.005474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.92840.31331060.29022692X-RAY DIFFRACTION100
1.9284-1.95850.29161440.27992647X-RAY DIFFRACTION100
1.9585-1.99060.31611550.26812648X-RAY DIFFRACTION100
1.9906-2.0250.25591320.25932647X-RAY DIFFRACTION100
2.025-2.06180.2551890.22922617X-RAY DIFFRACTION100
2.0618-2.10140.24711330.22372661X-RAY DIFFRACTION100
2.1014-2.14430.22681380.21192710X-RAY DIFFRACTION100
2.1443-2.19090.23921270.19742646X-RAY DIFFRACTION100
2.1909-2.24190.22661400.19442614X-RAY DIFFRACTION100
2.2419-2.29790.24481270.18092725X-RAY DIFFRACTION100
2.2979-2.360.19511250.17492640X-RAY DIFFRACTION100
2.36-2.42940.2161330.17012666X-RAY DIFFRACTION100
2.4294-2.50780.19961370.16272675X-RAY DIFFRACTION100
2.5078-2.59740.22161690.16642623X-RAY DIFFRACTION100
2.5974-2.70140.20411510.16752647X-RAY DIFFRACTION100
2.7014-2.82420.21541300.17362672X-RAY DIFFRACTION100
2.8242-2.9730.21061420.16972637X-RAY DIFFRACTION100
2.973-3.15910.23771280.16632679X-RAY DIFFRACTION100
3.1591-3.40280.17881650.15332633X-RAY DIFFRACTION100
3.4028-3.74470.12771550.13562627X-RAY DIFFRACTION100
3.7447-4.28530.13221610.12162637X-RAY DIFFRACTION100
4.2853-5.39440.13431340.12682664X-RAY DIFFRACTION100
5.3944-31.02440.15891030.18022708X-RAY DIFFRACTION100

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