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- PDB-4p3n: Structural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Sy... -

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Basic information

Entry
Database: PDB / ID: 4p3n
TitleStructural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Synthetase by Borrelidin 1
ComponentsThreonine--tRNA ligase, cytoplasmic
KeywordsLIGASE/LIGASE INHIBITOR / synthetase / inhibitor / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / Cytosolic tRNA aminoacylation / tRNA binding / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / 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-2CR / Threonine--tRNA ligase 1, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 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
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
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
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonine--tRNA ligase, cytoplasmic
B: Threonine--tRNA ligase, cytoplasmic
C: Threonine--tRNA ligase, cytoplasmic
D: Threonine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,09212
Polymers193,8724
Non-polymers2,2208
Water7,008389
1
A: Threonine--tRNA ligase, cytoplasmic
B: Threonine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0466
Polymers96,9362
Non-polymers1,1104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-104 kcal/mol
Surface area31920 Å2
MethodPISA
2
C: Threonine--tRNA ligase, cytoplasmic
D: Threonine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0466
Polymers96,9362
Non-polymers1,1104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-102 kcal/mol
Surface area31760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.870, 78.000, 118.050
Angle α, β, γ (deg.)86.990, 83.320, 84.390
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 48467.980 Da / Num. of mol.: 4 / Fragment: UNP residues 322-723
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TARS / Production host: Escherichia coli (E. coli) / References: UniProt: P26639, threonine-tRNA ligase
#2: 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 / Borrelidin


Mass: 489.644 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H43NO6 / Comment: antibiotic, inhibitor*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Calcium Acetate, PEG4000, Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.6→117.147 Å / Num. all: 67861 / Num. obs: 67861 / % possible obs: 98.1 % / Redundancy: 2.2 % / Biso Wilson estimate: 32.49 Å2 / Rpim(I) all: 0.085 / Rrim(I) all: 0.129 / Rsym value: 0.096 / Net I/av σ(I): 6.056 / Net I/σ(I): 5.8 / Num. measured all: 148431
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.2 % / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.6-2.740.3322.22150198360.2950.332297.5
2.74-2.910.2542.92054593880.2260.2542.697.7
2.91-3.110.18441917687810.1640.1843.697.9
3.11-3.360.1275.51794682070.1130.1274.998
3.36-3.680.0877.71646275250.0780.0876.798.2
3.68-4.110.066101499368470.0580.0668.298.4
4.11-4.750.05410.91322460470.0470.0549.998.5
4.75-5.810.069.91123451280.0530.069.698.6
5.81-8.220.0727.5862939370.0640.072998.6
8.22-65.9460.075.2472121650.0660.0711.198.7

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementResolution: 2.6→47.706 Å / FOM work R set: 0.7932 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.13 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 6731 5.08 %
Rwork0.2276 125744 -
obs0.229 132475 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.47 Å2 / Biso mean: 56.19 Å2 / Biso min: 17.16 Å2
Refinement stepCycle: final / Resolution: 2.6→47.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12973 0 144 390 13507
Biso mean--48.85 52.1 -
Num. residues----1608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813453
X-RAY DIFFRACTIONf_angle_d1.02718208
X-RAY DIFFRACTIONf_chiral_restr0.0721928
X-RAY DIFFRACTIONf_plane_restr0.0042391
X-RAY DIFFRACTIONf_dihedral_angle_d17.2444950
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.69290.37176070.3369123961300394
2.6929-2.80070.31626620.3119123581302094
2.8007-2.92820.31637590.2937123691312895
2.9282-3.08250.31286470.2814124691311695
3.0825-3.27560.29886760.2648125281320495
3.2756-3.52850.25226910.2387126201331196
3.5285-3.88340.24086470.213126821332996
3.8834-4.4450.20337100.1787126791338997
4.445-5.59880.20076660.1714128541352097
5.5988-47.71430.24146660.2042127891345597
Refinement TLS params.Method: refined / Origin x: -11.4608 Å / Origin y: 17.0153 Å / Origin z: -26.1997 Å
111213212223313233
T0.3381 Å2-0.078 Å20.0942 Å2-0.1121 Å20.0174 Å2--0.1866 Å2
L0.1604 °2-0.0461 °20.0247 °2-0.3773 °2-0.1908 °2--0.3961 °2
S-0.0191 Å °0.0262 Å °0.0193 Å °-0.0605 Å °0.0257 Å °-0.0412 Å °-0.0547 Å °0.0005 Å °0.0086 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA322 - 801
2X-RAY DIFFRACTION1allB322 - 801
3X-RAY DIFFRACTION1allC322 - 801
4X-RAY DIFFRACTION1allD322 - 801
5X-RAY DIFFRACTION1allF2 - 557

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