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- PDB-9lot: Crystal structure of Escherichia coli trptophanyl-tRNA synthetase... -

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Basic information

Entry
Database: PDB / ID: 9lot
TitleCrystal structure of Escherichia coli trptophanyl-tRNA synthetase in complex with N-piperidine ibrutinib
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / trptophanyl-tRNA synthetase / N-piperidine ibrutinib / complex
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
: / CHLORZOXAZONE / TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsPeng, X. / Chen, B. / Xia, K. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177140 China
CitationJournal: To Be Published
Title: The lineage-specific tRNA recognition mechanism of bacterial trptophanyl-tRNA synthetase and its implications for inhibitor discover
Authors: Peng, X. / Xia, K. / Huang, Q. / Xiang, M. / Han, L. / Qiu, H. / Gu, Q. / Chen, B. / Zhou, H.
History
DepositionJan 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,1258
Polymers76,7472
Non-polymers1,3786
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-75 kcal/mol
Surface area25910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.768, 79.649, 78.361
Angle α, β, γ (deg.)90.00, 105.78, 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 (E. coli)
Gene: trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915, BMT91_03555, BvCmsNSP007_00090, BXT93_04920, C0P57_000786, C2R31_ ...Gene: trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915, BMT91_03555, BvCmsNSP007_00090, BXT93_04920, C0P57_000786, C2R31_002885, C3F40_19370, CG704_07870, CIG67_21025, CTR35_001866, D9D43_04205, DD762_12005, DL968_00250, DNQ45_04190, DTL43_13995, DU321_12325, E4K51_10330, E6D34_04225, EIA08_11870, EPS97_04620, F7F11_12075, F7N46_14665, F9413_17445, F9461_03030, F9B07_12605, FGAF848_25410, FKO60_13960, FOI11_018845, FOI11_04335, FPS11_03390, FZU14_04195, G3V95_06005, G4A38_16925, G4A47_18515, G5603_11025, GAI89_06310, GNW61_08470, GOP25_12480, GP944_08250, GQE86_01825, GQN24_10725, HEP34_002452, HI055_002233, HJQ60_002846, HL563_11055, HL601_09110, HLX92_09755, HLZ50_06610, HMV95_07850, HVW04_17215, HVW43_18350, HVY77_01760, I6H00_19775, IH772_08800, J0541_002134, JNP96_25720, NCTC10764_03793, NCTC10974_00460, NCTC9044_01447, NCTC9073_00479, NCTC9077_00527, NCTC9706_02656, P6223_000209, Q2V20_09290, QDW62_01780, QO046_14075, R8G00_13645, SAMEA3472044_01080, SAMEA3472056_01981, SAMEA3752557_02035
Production host: Escherichia coli (E. coli) / References: UniProt: E2QFN4, tryptophan-tRNA ligase

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Non-polymers , 5 types, 476 molecules

#2: Chemical ChemComp-A1EKY / 3-(4-phenoxyphenyl)-1-piperidin-4-yl-pyrazolo[3,4-d]pyrimidin-4-amine / N-piperidine Ibrutinib


Mass: 386.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N6O / 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-CLW / CHLORZOXAZONE / 5-CHLORO-2-BENZOXAZOLONE


Mass: 169.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4ClNO2
#5: Chemical ChemComp-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N7O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.15 M ammonium sulfate, 0.1M HEPES pH 7.5, 25% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.59→75.41 Å / Num. obs: 98739 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9
Reflection shellResolution: 1.59→1.67 Å / Rmerge(I) obs: 1.535 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 14351

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
autoPROCdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8I1Y

8i1y


Resolution: 1.59→54.49 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.009 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20487 4705 4.9 %RANDOM
Rwork0.18908 ---
obs0.18985 92139 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.836 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å2-0 Å2-0.25 Å2
2--1.55 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 1.59→54.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 92 470 5520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135154
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174666
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.6327010
X-RAY DIFFRACTIONr_angle_other_deg1.5841.58610772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3675650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40722.946241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11815808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7021525
X-RAY DIFFRACTIONr_chiral_restr0.0620.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021049
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_it1.4152.3912612
X-RAY DIFFRACTIONr_mcbond_other1.4152.392611
X-RAY DIFFRACTIONr_mcangle_it2.0843.5783258
X-RAY DIFFRACTIONr_mcangle_other2.0843.5793259
X-RAY DIFFRACTIONr_scbond_it1.9542.5642542
X-RAY DIFFRACTIONr_scbond_other1.9542.5562531
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9733.753735
X-RAY DIFFRACTIONr_long_range_B_refined3.84829.2565867
X-RAY DIFFRACTIONr_long_range_B_other3.81428.9695772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.627 Å
RfactorNum. reflection% reflection
Rfree0.35 272 -
Rwork0.325 5550 -
obs--79.42 %

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