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- PDB-4ttv: Crystal structure of human ThrRS complexing with a bioengineered ... -

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Basic information

Entry
Database: PDB / ID: 4ttv
TitleCrystal structure of human ThrRS complexing with a bioengineered macrolide BC194
ComponentsThreonine--tRNA ligase, cytoplasmic
KeywordsLIGASE/ANTIBIOTIC / tRNA / synthetase / inhibitor / macrolide / LIGASE-ANTIBIOTIC 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 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-BC9 / Threonine--tRNA ligase 1, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFang, P. / 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: Sci Rep / Year: 2015
Title: Aminoacyl-tRNA synthetase dependent angiogenesis revealed by a bioengineered macrolide inhibitor.
Authors: Mirando, A.C. / Fang, P. / Williams, T.F. / Baldor, L.C. / Howe, A.K. / Ebert, A.M. / Wilkinson, B. / Lounsbury, K.M. / Guo, M. / Francklyn, C.S.
History
DepositionJun 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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)195,81612
Polymers193,6444
Non-polymers2,1728
Water1,11762
1
A: Threonine--tRNA ligase, cytoplasmic
B: Threonine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9086
Polymers96,8222
Non-polymers1,0864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-100 kcal/mol
Surface area31930 Å2
MethodPISA
2
C: Threonine--tRNA ligase, cytoplasmic
D: Threonine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9086
Polymers96,8222
Non-polymers1,0864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-101 kcal/mol
Surface area31470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.020, 134.610, 128.670
Angle α, β, γ (deg.)90.000, 90.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 48410.930 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-BC9 / (1R,2R)-2-[(2S,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadec-6-en-2-yl]cyclobutanecarboxylic acid


Mass: 477.633 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H43NO6
#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


Mass: 18.015 Da / Num. of mol.: 62 / 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: 4.12 Å3/Da / Density % sol: 70.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tris, PEG8000

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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: Oct 7, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.8→128.67 Å / Num. all: 77181 / Num. obs: 77181 / % possible obs: 100 % / Redundancy: 3.2 % / Biso Wilson estimate: 49.29 Å2 / Rpim(I) all: 0.097 / Rrim(I) all: 0.177 / Rsym value: 0.147 / Net I/av σ(I): 3.765 / Net I/σ(I): 5.2 / Num. measured all: 248742
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.953.20.8890.936319112110.5810.8891.3100
2.95-3.133.20.581.334405106260.3790.582100
3.13-3.353.20.37223219299910.2430.3722.8100
3.35-3.613.20.2432.42991993240.1610.2434.2100
3.61-3.963.20.15432736985870.1030.1545.9100
3.96-4.433.20.0957.12488777610.0620.0957.6100
4.43-5.113.20.0718.82215068700.0470.0719100
5.11-6.263.30.0719.31888557990.0460.0718.8100
6.26-8.853.30.05610.81467345050.0370.0569.599.9
8.85-49.133.20.0435.7794325070.0330.04312.199.2

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P3N

4p3n


Resolution: 2.8→46.506 Å / FOM work R set: 0.6956 / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2882 3850 5.01 %
Rwork0.2548 72920 -
obs0.2565 76770 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.03 Å2 / Biso mean: 57.39 Å2 / Biso min: 26.22 Å2
Refinement stepCycle: final / Resolution: 2.8→46.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13045 0 140 62 13247
Biso mean--49.99 46.38 -
Num. residues----1612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713517
X-RAY DIFFRACTIONf_angle_d1.21818282
X-RAY DIFFRACTIONf_chiral_restr0.0431928
X-RAY DIFFRACTIONf_plane_restr0.0042401
X-RAY DIFFRACTIONf_dihedral_angle_d15.2244996
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 (%)
2.8-2.90010.3953580.382172587616100
2.9001-3.01620.38313790.36772937672100
3.0162-3.15340.36583940.334972967690100
3.1534-3.31960.36693780.312672567634100
3.3196-3.52750.33534080.301672717679100
3.5275-3.79980.31523850.268573397724100
3.7998-4.18190.25983820.236372877669100
4.1819-4.78650.24533600.198773597719100
4.7865-6.02850.23354360.202772917727100
6.0285-46.51260.23013700.2037270764097
Refinement TLS params.Method: refined / Origin x: 22.889 Å / Origin y: -29.0578 Å / Origin z: 32.1798 Å
111213212223313233
T0.2366 Å2-0.0026 Å2-0.0161 Å2-0.462 Å20.031 Å2--0.2845 Å2
L0.1586 °20.0131 °2-0.0052 °2-1.0337 °20.509 °2--0.6249 °2
S-0.0744 Å °0.008 Å °-0.0008 Å °-0.014 Å °0.0318 Å °0.1479 Å °-0.0022 Å °-0.2553 Å °0.036 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA321 - 723
2X-RAY DIFFRACTION1allA1
3X-RAY DIFFRACTION1allA991
4X-RAY DIFFRACTION1allB321 - 723
5X-RAY DIFFRACTION1allB1
6X-RAY DIFFRACTION1allB991
7X-RAY DIFFRACTION1allC321 - 723
8X-RAY DIFFRACTION1allC1
9X-RAY DIFFRACTION1allC991
10X-RAY DIFFRACTION1allD321 - 723
11X-RAY DIFFRACTION1allD1
12X-RAY DIFFRACTION1allD991
13X-RAY DIFFRACTION1allE1 - 63

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