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

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Basic information

Entry
Database: PDB / ID: 9lpd
TitleCrystal structure of Escherichia coli trptophanyl-tRNA synthetase in complex with tirabrutinib
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / trptophayl-tRNA synthetase / Tirabrutinib / 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: 2.05 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 24, 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

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)78,1938
Polymers76,7472
Non-polymers1,4466
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-73 kcal/mol
Surface area26380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.773, 79.435, 79.278
Angle α, β, γ (deg.)90.00, 105.71, 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, 185 molecules

#2: Chemical ChemComp-A1EK0 / Tirabrutinib / Btk Kinase inhibitor


Mass: 454.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H22N6O3 / 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.: 179 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
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: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.05→76.32 Å / Num. obs: 46067 / % possible obs: 98.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.052 / Rrim(I) all: 0.093 / Net I/σ(I): 8.4
Reflection shellResolution: 2.05→2.16 Å / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6713 / Rpim(I) all: 0.306 / Rrim(I) all: 0.565

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8I1Y

8i1y


Resolution: 2.05→30.65 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 2291 4.98 %RANDOM
Rwork0.232 ---
obs0.233 45967 98.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→30.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4977 0 97 180 5254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115178
X-RAY DIFFRACTIONf_angle_d1.2537040
X-RAY DIFFRACTIONf_dihedral_angle_d21.1271847
X-RAY DIFFRACTIONf_chiral_restr0.075791
X-RAY DIFFRACTIONf_plane_restr0.006930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.35861320.36982774X-RAY DIFFRACTION99
2.09-2.140.38771210.35052729X-RAY DIFFRACTION98
2.14-2.190.31261380.33012736X-RAY DIFFRACTION99
2.19-2.250.36641340.31472695X-RAY DIFFRACTION99
2.25-2.320.27471530.29772730X-RAY DIFFRACTION99
2.32-2.390.32051560.28752742X-RAY DIFFRACTION99
2.39-2.480.33771340.27352722X-RAY DIFFRACTION98
2.48-2.580.31761490.26522739X-RAY DIFFRACTION99
2.58-2.690.24111230.25352686X-RAY DIFFRACTION97
2.69-2.840.26921410.25242747X-RAY DIFFRACTION98
2.84-3.010.27621460.25882694X-RAY DIFFRACTION98
3.01-3.250.27431560.23622742X-RAY DIFFRACTION99
3.25-3.570.24651450.22692740X-RAY DIFFRACTION99
3.57-4.090.20571630.19022689X-RAY DIFFRACTION98
4.09-5.150.18691480.17772753X-RAY DIFFRACTION98
5.15-30.650.22421520.19622758X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0099-0.0215-0.0424-0.0272-0.01730.0034-0.11070.1856-0.130.03430.0803-0.0371-0.0833-0.0642-00.2101-0.03250.00350.3319-0.02870.208730.2956-4.4796-4.2004
20.11260.0739-0.04150.2149-0.13020.1775-0.07560.15750.0178-0.03320.13190.02570.01340.0668-00.2038-0.04230.00840.302-0.02350.152923.488-8.5571-3.8432
30.1448-0.01690.04660.0774-0.2470.0559-0.0661-0.03940.16520.0429-0.02530.02620.03260.046400.1881-0.0234-0.03620.1811-0.04180.273220.00033.367511.525
4-0.00040.0419-0.00430.01930.09560.02680.00040.0111-0.0260.1015-0.0875-0.1111-0.1670.0306-00.2148-0.0191-0.01350.31050.00180.282633.903-0.34195.9715
5-0.00550.0030.0208-0.0061-0.01750.02060.01960.04820.46490.2830.1798-0.0102-0.0138-0.3473-00.3530.02770.06020.5798-0.05970.495332.01086.4245-16.8863
60.0548-0.0076-0.17160.0963-0.00120.12990.0347-0.10410.0121-0.0035-0.2035-0.1118-0.0121-0.141700.3439-0.00790.0020.41990.03460.29648.42766.2725-20.2965
70.01680.07190.0862-0.03340.03770.0331-0.26690.68060.2614-0.3225-0.6349-1.17210.0293-0.0328-00.4081-0.07920.14690.4198-0.4846-0.279234.9565-7.7348-20.8473
80.08030.1268-0.0564-0.1133-0.02380.0367-0.0918-0.2265-0.33590.08080.12860.10310.19690.230400.2189-0.0087-0.01330.1981-0.08040.281114.9298-15.32999.8869
90.4763-0.0013-0.2436-0.0264-0.3698-0.00980.02180.02420.21380.09920.05110.04810.0281-0.0767-00.16440.00550.00020.1558-0.01120.2601-4.15110.71614.6989
100.0439-0.08290.30990.15150.5741-0.0349-0.0704-0.2732-0.0319-0.36230.14910.0786-0.12140.0762-00.43390.00190.0650.2542-0.00430.2489-18.3379.09834.8368
110.08550.0446-0.04810.06420.12080.0179-0.02610.1469-0.0816-0.030.0920.09390.1553-0.06800.2492-0.0293-0.01660.3046-0.00770.26430.3592-13.44128.4025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 86 )
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 168 )
4X-RAY DIFFRACTION4chain 'A' and (resid 169 through 189 )
5X-RAY DIFFRACTION5chain 'A' and (resid 190 through 212 )
6X-RAY DIFFRACTION6chain 'A' and (resid 213 through 269 )
7X-RAY DIFFRACTION7chain 'A' and (resid 270 through 298 )
8X-RAY DIFFRACTION8chain 'A' and (resid 299 through 335 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 183 )
10X-RAY DIFFRACTION10chain 'B' and (resid 184 through 298 )
11X-RAY DIFFRACTION11chain 'B' and (resid 299 through 334 )

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