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- PDB-4hws: Crystal structure of E. coli Threonyl-tRNA synthetase bound to a ... -

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Basic information

Entry
Database: PDB / ID: 4hws
TitleCrystal structure of E. coli Threonyl-tRNA synthetase bound to a novel inhibitor
ComponentsThreonine--tRNA ligase
KeywordsLigase/Ligase Inhibitor / aminoacyl-tRNA synthetase / protein-inhibitor complex / antibacterial / Ligase-Ligase Inhibitor complex
Function / homology
Function and homology information


tRNA aminoacylation / aminoacyl-tRNA ligase activity / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding ...tRNA aminoacylation / aminoacyl-tRNA ligase activity / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding / regulation of translation / tRNA binding / response to antibiotic / protein homodimerization activity / RNA binding / zinc ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Anticodon-binding domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Anticodon-binding domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Beta-grasp domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1B3 / Threonine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsHilgers, M.T.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Identification of bacteria-selective threonyl-tRNA synthetase substrate inhibitors by structure-based design.
Authors: Teng, M. / Hilgers, M.T. / Cunningham, M.L. / Borchardt, A. / Locke, J.B. / Abraham, S. / Haley, G. / Kwan, B.P. / Hall, C. / Hough, G.W. / Shaw, K.J. / Finn, J.
History
DepositionNov 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,0006
Polymers95,9972
Non-polymers1,0034
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-16 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.181, 110.327, 114.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 242 - 638 / Label seq-ID: 3 - 399

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Threonine--tRNA ligase / Threonyl-tRNA synthetase / ThrRS


Mass: 47998.594 Da / Num. of mol.: 2 / Fragment: UNP residues 242-642
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: thrS, b1719, JW1709 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: P0A8M3, threonine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-1B3 / N-{[3-(4-amino-2-chloroquinazolin-7-yl)phenyl]sulfonyl}-L-threoninamide


Mass: 435.885 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18ClN5O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: PEG 4000, MPD, sodium citrate, pH 5.9, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.698→50 Å / Num. obs: 104555

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.35 Å
Translation2.5 Å33.35 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→33.35 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.794 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 5500 5 %RANDOM
Rwork0.1965 ---
obs0.1976 104555 90.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.45 Å2 / Biso mean: 29.667 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 60 544 7209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196815
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9569186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44923.501357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29151230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7851562
X-RAY DIFFRACTIONr_chiral_restr0.1060.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215240
Refine LS restraints NCS

Ens-ID: 1 / Number: 477 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 158 -
Rwork0.469 2688 -
all-2846 -
obs--32.71 %
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)
10.6722-0.0461-0.140.368-0.0320.19110.029-0.06660.0196-0.0016-0.00910.02370.0152-0.0028-0.01990.18160.0037-0.0010.1904-0.0140.190218.1175-27.982-17.3637
21.1632-0.8877-0.68531.7036-0.2611.8433-0.1072-0.1684-0.06360.07640.09770.04450.07350.14050.00950.16570.0041-0.01470.20340.01920.185123.8273-36.5061-13.1133
32.884-0.71590.92460.4338-0.340.4657-0.0559-0.0271-0.03710.04410.00480.0377-0.0041-0.03060.05110.1817-0.0049-0.00180.1933-0.00380.201914.6399-32.5941-19.2003
40.9451-0.3941-0.6170.41930.11810.5409-0.01010.1686-0.0739-0.1252-0.0580.07990.0742-0.10930.06810.1918-0.0145-0.01860.2137-0.04380.20098.1243-38.8869-32.1399
51.139-0.9738-0.19592.1480.06151.8914-0.1013-0.1146-0.1260.18050.10780.08830.16970.0523-0.00660.1912-0.03060.01890.1718-0.01060.22011.2361-44.6306-11.5677
60.6111-0.0487-0.80610.8432-0.30961.2909-0.00290.0651-0.09860.01870.00310.05470.0207-0.0745-0.00010.1808-0.0376-0.00280.1758-0.04060.22331.9442-44.9932-21.4331
70.2235-0.108-0.23550.62650.04180.287-0.03420.0084-0.06470.0316-0.02020.06190.0884-0.05980.05440.1808-0.01210.00250.1962-0.01730.22079.2407-38.3197-19.781
812.8646-5.60892.92282.5095-1.86146.3728-0.07670.20320.03330.02440.0035-0.00430.2528-0.67620.07320.0782-0.01270.04760.2988-0.01990.3077-11.6793-22.6073-19.2906
90.2924-0.1218-0.34960.31230.11610.4280.0383-0.0224-0.0109-0.0901-0.0355-0.0803-0.03530.0092-0.00280.21250.00680.02470.18030.00630.219736.9613-31.8412-36.8833
100.8748-0.4241-0.35341.6185-1.15491.8530.0119-0.0432-0.0323-0.2487-0.0676-0.31760.08350.12150.05570.22210.00950.0910.1651-0.02080.258845.5852-35.1886-43.1755
112.31670.8432-1.05383.5449-2.58782.0219-0.320.3207-0.2706-0.3420.2316-0.19820.2073-0.21810.08840.332-0.07590.1940.2147-0.08070.222542.5279-36.4929-50.7696
120.92390.6932-0.43382.0111-0.87191.8636-0.06460.2387-0.1379-0.4176-0.00860.03230.0955-0.06740.07320.2570.0140.0170.1959-0.02450.137430.0625-37.0018-45.6844
130.64860.1530.14880.22020.15830.38020.0611-0.0454-0.0213-0.0384-0.03840.0557-0.00320.0052-0.02270.1864-0.00250.01480.17240.00470.195623.9011-15.0315-17.5017
141.12680.40740.53660.6154-0.35491.15060.0921-0.2199-0.00370.2973-0.14520.0157-0.08320.05090.05310.31230.00690.00890.24530.03280.144429.3773-24.7028-0.2044
151.2845-0.3196-0.67160.31730.35170.73630.0009-0.08130.00730.00940.0288-0.04220.07090.0959-0.02960.17690.00540.00420.208-0.00720.210641.0551-22.623-17.9087
162.1767-1.10310.95021.5515-0.21112.0262-0.1034-0.25720.07130.0210.12020.0474-0.07-0.1227-0.01680.1726-0.00640.03980.2097-0.0240.193522.3677-10.2228-8.2376
170.5939-0.15560.02940.60740.1120.10070.02010.03980.0369-0.0765-0.0016-0.0323-0.07860.0803-0.01860.2006-0.0250.02940.201-0.00110.200739.3762-5.716-23.8804
181.166-0.89390.57012.551-2.1943.4687-0.0021-0.04990.1140.2615-0.1655-0.1196-0.30450.2990.16750.1942-0.07310.00640.198-0.00330.162647.4234-3.6128-8.1837
190.1670.1406-0.21852.5189-2.02662.52210.03310.0114-0.00710.1141-0.0160.0477-0.13770.0425-0.01710.2113-0.04360.03060.1738-0.00770.196741.91960.4367-13.2151
200.11380.15630.02490.48320.3430.39110.0684-0.08370.07860.0122-0.03430.0052-0.09820.1173-0.03410.1728-0.02480.0240.2127-0.00130.237337.52-7.5295-14.0059
2120.24032.2252-13.7756.63145.109616.24820.37240.11810.07780.11760.5267-0.726-0.22560.5049-0.89910.0270.04330.01570.4231-0.03750.325260.8349-22.2449-19.6607
221.325-0.51220.02950.4520.08530.120.01930.0220.0385-0.0111-0.0290.0168-0.10140.06050.00970.203-0.01090.02050.1794-0.0050.216329.1356-7.2305-20.204
230.4785-0.07920.01071.0003-0.17520.504-0.00860.02780.0567-0.1067-0.00380.1150.05420.03440.01230.20480.0308-0.02410.16540.01070.20975.4591-7.4799-41.7474
244.1194-2.09560.7418.6557-1.3686.0330.02650.50580.28510.2873-0.2926-0.3301-0.56590.10680.26610.20090.0320.00770.21150.04460.174622.4859-2.8556-38.8297
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A242 - 357
2X-RAY DIFFRACTION2A358 - 373
3X-RAY DIFFRACTION3A374 - 389
4X-RAY DIFFRACTION4A390 - 418
5X-RAY DIFFRACTION5A419 - 432
6X-RAY DIFFRACTION6A433 - 465
7X-RAY DIFFRACTION7A466 - 499
8X-RAY DIFFRACTION8A500 - 507
9X-RAY DIFFRACTION9A508 - 582
10X-RAY DIFFRACTION10A583 - 601
11X-RAY DIFFRACTION11A602 - 619
12X-RAY DIFFRACTION12A620 - 650
13X-RAY DIFFRACTION13B242 - 312
14X-RAY DIFFRACTION14B313 - 326
15X-RAY DIFFRACTION15B327 - 360
16X-RAY DIFFRACTION16B361 - 380
17X-RAY DIFFRACTION17B381 - 418
18X-RAY DIFFRACTION18B419 - 445
19X-RAY DIFFRACTION19B446 - 466
20X-RAY DIFFRACTION20B467 - 498
21X-RAY DIFFRACTION21B499 - 505
22X-RAY DIFFRACTION22B506 - 531
23X-RAY DIFFRACTION23B532 - 632
24X-RAY DIFFRACTION24B633 - 639

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