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

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Basic information

Entry
Database: PDB / ID: 4hwo
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


aminoacyl-tRNA ligase activity / tRNA aminoacylation / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA deacylase activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding ...aminoacyl-tRNA ligase activity / tRNA aminoacylation / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA deacylase 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 / cytosol / cytoplasm
Similarity search - Function
Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Anticodon-binding domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS-like ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Anticodon-binding domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS-like / TGS domain profile. / TGS / 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. / Beta-grasp domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-409 / Threonine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.907 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)96,9316
Polymers95,9972
Non-polymers9344
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-17 kcal/mol
Surface area32640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.900, 110.300, 114.360
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-409 / N-{[3-(4-aminoquinazolin-7-yl)phenyl]sulfonyl}-L-threoninamide


Mass: 401.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19N5O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.82 Å3/Da / Density % sol: 56.41 %
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 / Details: Mar345
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.907→79.39 Å / Num. all: 82308 / Num. obs: 82308 / % possible obs: 95.3 % / Redundancy: 7.5 % / Rsym value: 0.055 / Net I/σ(I): 24.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.907-26.50.2263.467090103330.22682.7
2-2.1270.1544.978806112730.15495.5
2.12-2.277.20.1096.877046106570.10996
2.27-2.457.50.0838.875746100330.08396.8
2.45-2.687.90.06610.77330493220.06697.4
2.68-380.05412.56832785170.05498.2
3-3.468.10.045146146575780.04598.6
3.46-4.248.10.04114.55274865140.04199.3
4.24-680.03914.34103551170.03999.6
6-43.7037.40.04310.12191229640.04399.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.907→37.78 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.802 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 4111 5 %RANDOM
Rwork0.184 ---
obs0.1848 82237 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.6 Å2 / Biso mean: 24.402 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0 Å2
2---0.09 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.907→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 58 545 7208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196813
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9569182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2085805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69623.501357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.447151230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.931562
X-RAY DIFFRACTIONr_chiral_restr0.1060.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215238
Refine LS restraints NCS

Ens-ID: 1 / Number: 486 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.907→1.956 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 242 -
Rwork0.306 5065 -
all-5307 -
obs--89.4 %
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)
10.97350.0736-0.21170.48840.01860.34950.02390.10430.0417-0.0018-0.0024-0.03020.02240.0122-0.02150.12640.002-0.0040.12320.01240.1114-18.0503-27.992717.3104
22.06871.1311-0.77820.79670.19882.508-0.14520.2281-0.1016-0.08110.1209-0.06350.0731-0.15820.02430.11370.0071-0.02160.1406-0.02850.1255-23.681-36.643613.1039
34.10171.18380.92190.73980.45960.5281-0.01590.0074-0.0786-0.0355-0.0128-0.0454-0.00030.04850.02870.12370.0138-0.00720.12360.00640.1277-14.6023-32.591219.1859
41.55521.1139-1.01861.1522-0.49510.84170.0494-0.2236-0.09010.1326-0.0936-0.11660.02340.15350.04420.13060.0204-0.03060.16690.0350.1266-8.063-38.88332.1223
53.19890.9786-0.24091.6736-0.85462.9943-0.09110.2169-0.1664-0.24280.112-0.03830.1683-0.0275-0.02090.16170.03250.00810.10.00030.1445-1.2705-44.62811.5161
60.89860.083-1.14971.33720.26532.4406-0.0256-0.0672-0.0633-0.04040.0303-0.0009-0.08640.071-0.00470.12610.0525-0.01070.1270.03010.1365-1.9144-44.992521.406
70.7730.3144-0.33060.648-0.02850.3934-0.01430.0359-0.0667-0.0185-0.0333-0.07920.10880.07190.04760.12580.01770.00120.13230.01760.1482-9.1747-38.329619.7514
812.64646.8103-0.88674.03271.503310.8086-0.2218-0.2301-0.4071-0.12290.088-0.19680.01981.11620.13380.05440.02930.02240.24480.03380.226611.6745-22.677219.2435
90.6595-0.0296-0.47050.45480.01010.36940.0251-0.0262-0.00910.1237-0.04540.1129-0.02540.03430.02030.1674-0.00490.03110.1089-0.01170.1416-36.9375-31.879736.7429
102.27960.188-1.46393.17222.06043.7411-0.0252-0.0106-0.09120.3578-0.09020.55040.0307-0.12120.11540.1789-0.00930.11010.09410.02020.2023-45.6214-35.235443.0325
113.7808-2.4703-4.25858.00857.5448.5351-0.4977-0.5223-0.4920.37930.13830.37440.24910.41680.35950.61160.14070.3920.160.11530.2626-42.6595-36.595150.5913
123.8765-2.4297-1.20554.46430.30362.1476-0.1844-0.4434-0.11830.59340.11670.12560.00340.28210.06770.2462-0.01670.00050.1589-0.01160.0574-30.9891-32.276448.39
131.0164-0.01220.24190.4442-0.12040.65060.05810.0583-0.02930.0348-0.0325-0.07160.00910.0141-0.02570.12030.00770.01390.1013-0.00940.1136-23.8488-15.041517.4423
142.1251-0.14650.66225.54941.29811.69140.10690.2885-0.134-0.5402-0.0846-0.0220.0009-0.088-0.02230.1829-0.00640.00170.2219-0.03050.0807-29.2887-24.77180.1677
152.45380.1397-0.75210.2936-0.211.38570.01540.0831-0.02540.02970.02330.07820.0967-0.1209-0.03860.1279-0.00830.00430.11970.00470.1246-40.9319-22.665917.8695
163.03362.08231.20512.58880.49943.3552-0.12460.25520.1259-0.07650.1337-0.0316-0.17390.1087-0.0090.11340.0160.03010.14760.02270.12-22.333-10.18668.1912
170.73190.2211-0.15871.0199-0.17190.08360.0094-0.03630.050.13990.01790.08-0.0737-0.0503-0.02730.16820.03480.0280.1464-0.00490.1212-39.3212-5.712723.8036
181.36451.00270.84343.6893.62425.72790.04880.06680.0735-0.2306-0.18490.1355-0.2337-0.36840.13610.13010.06630.00010.14350.00040.0861-47.3788-3.69798.1666
190.3367-0.4432-0.28764.54123.62375.40730.02350.0133-0.0102-0.16080.0204-0.0674-0.15280.057-0.04390.12740.03290.02760.11080.0070.1157-41.88540.451113.1152
200.77310.2908-0.08131.0371-0.28130.38710.00730.14590.1791-0.0253-0.00050.0787-0.0795-0.1051-0.00680.12080.0130.01760.1510.01580.1297-37.4423-7.585213.9017
2153.2307-18.538-38.035735.94810.496934.89160.40330.6275-0.0338-0.90651.20351.9793-0.589-2.6457-1.60680.19510.33770.17081.24230.53610.4588-60.8051-22.321519.6731
222.3580.7644-0.05810.6691-0.10310.2610.0173-0.01830.1292-0.0045-0.04220.0141-0.0904-0.03850.02490.15060.01750.01420.11230.0050.1333-29.0675-7.220920.1079
230.6967-0.00860.171.4370.18030.7253-0.0148-0.01930.04870.15580.005-0.10730.0484-0.03170.00980.1606-0.0284-0.03110.11-0.00840.1222-5.3678-7.377641.5731
248.1616-1.75855.32814.48295.085412.9806-0.4413-0.6127-0.0867-0.35920.3010.2017-1.0116-0.10210.14030.2417-0.07760.06630.1768-0.07610.1787-22.0881-2.896338.6953
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 - 642
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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