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- PDB-4p3o: Structural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Sy... -

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Basic information

Entry
Database: PDB / ID: 4p3o
TitleStructural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Synthetase by Borrelidin 2
ComponentsThreonine--tRNA ligase
KeywordsLIGASE/LIGASE INHIBITOR / synthetase / inhibitor / 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 / cytosol / cytoplasm
Similarity search - Function
Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / Threonyl/alanyl tRNA synthetase, SAD / TGS domain / 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 / : / Threonyl/alanyl tRNA synthetase, SAD / TGS domain / 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-2CR / Threonine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.505 Å
AuthorsFang, P. / Yu, X. / Chen, K. / Chen, X. / Guo, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100136 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106134 United States
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for full-spectrum inhibition of translational functions on a tRNA synthetase.
Authors: Fang, P. / Yu, X. / Jeong, S.J. / Mirando, A. / Chen, K. / Chen, X. / Kim, S. / Francklyn, C.S. / Guo, M.
History
DepositionMar 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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

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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)97,42611
Polymers95,8552
Non-polymers1,5719
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-103 kcal/mol
Surface area31970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.449, 107.617, 109.209
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 47927.516 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) / Gene: thrS, b1719, JW1709 / Production host: Escherichia coli (E. coli) / 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-2CR / (1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadeca-4,6-dien-2-yl]cyclopentanecarboxylic acid / Borrelidin


Mass: 489.644 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H43NO6 / Comment: antibiotic, inhibitor*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.9 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG400, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 36592 / % possible obs: 93.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 27.56 Å2 / Rmerge(I) obs: 0.104 / Χ2: 0.965 / Net I/av σ(I): 14.611 / Net I/σ(I): 5.9 / Num. measured all: 213704
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.5950.51134080.91889.3
2.59-2.694.90.42434051.0888.2
2.69-2.824.90.32231090.90881.5
2.82-2.965.50.26835470.90791.5
2.96-3.155.70.20337320.90396.9
3.15-3.395.90.14838510.99299.5
3.39-3.736.40.11738801.13399.7
3.73-4.276.50.07538891.01799.5
4.27-5.386.10.05237240.91194.4
5.38-506.90.04640470.87197.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementResolution: 2.505→35.719 Å / FOM work R set: 0.8474 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 1744 5 %
Rwork0.1982 33102 -
obs0.1997 34846 89.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.49 Å2 / Biso mean: 35.94 Å2 / Biso min: 10 Å2
Refinement stepCycle: final / Resolution: 2.505→35.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6497 0 102 351 6950
Biso mean--35.34 38.17 -
Num. residues----802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046782
X-RAY DIFFRACTIONf_angle_d0.9279139
X-RAY DIFFRACTIONf_chiral_restr0.067963
X-RAY DIFFRACTIONf_plane_restr0.0031189
X-RAY DIFFRACTIONf_dihedral_angle_d13.7362588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.505-2.57850.2886970.25061893199062
2.5785-2.66170.26221250.23992240236574
2.6617-2.75680.2831200.24712352247277
2.7568-2.86710.27791490.242405255479
2.8671-2.99760.27851280.23742818294692
2.9976-3.15550.25081470.22772952309996
3.1555-3.35310.2321700.2133038320899
3.3531-3.61170.21541600.194630683228100
3.6117-3.97480.22451590.179130923251100
3.9748-4.54890.18511440.15553081322599
4.5489-5.72740.19131660.17352897306393
5.7274-35.72280.19981790.192732663445100
Refinement TLS params.Method: refined / Origin x: 20.7117 Å / Origin y: 30.3794 Å / Origin z: 20.7998 Å
111213212223313233
T0.085 Å2-0.0248 Å20.0027 Å2-0.0708 Å20.0043 Å2--0.0617 Å2
L0.5373 °2-0.0637 °2-0.0526 °2-0.5224 °20.0144 °2--0.3725 °2
S0.0108 Å °-0.0303 Å °0.0081 Å °0.0947 Å °-0.0206 Å °0.0262 Å °0.0024 Å °0.0057 Å °0.0163 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA242 - 642
2X-RAY DIFFRACTION1allA650
3X-RAY DIFFRACTION1allD1
4X-RAY DIFFRACTION1allB242 - 642
5X-RAY DIFFRACTION1allB650
6X-RAY DIFFRACTION1allE1
7X-RAY DIFFRACTION1allF1 - 664
8X-RAY DIFFRACTION1allG1
9X-RAY DIFFRACTION1allH1
10X-RAY DIFFRACTION1allI1
11X-RAY DIFFRACTION1allJ1
12X-RAY DIFFRACTION1allK1

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