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- PDB-3p0i: Leishmania major Tyrosyl-tRNA synthetase in complex with tyrosino... -

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Basic information

Entry
Database: PDB / ID: 3p0i
TitleLeishmania major Tyrosyl-tRNA synthetase in complex with tyrosinol, cubic crystal form
ComponentsTyrosyl-tRNA synthetase
KeywordsLIGASE / aminoacyl-tRNA synthetase / tRNA ligase / aaRS / TyrRS / pseudodimer / translation / ATP-binding / nucleotide-binding / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ciliary plasm / ATP binding / cytoplasm
Similarity search - Function
Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-[(2S)-2-amino-3-hydroxypropyl]phenol / tyrosine--tRNA ligase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 3.13 Å
AuthorsMerritt, E.A. / Larson, E.T. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Double-Length Tyrosyl-tRNA Synthetase from the Eukaryote Leishmania major Forms an Intrinsically Asymmetric Pseudo-Dimer.
Authors: Larson, E.T. / Kim, J.E. / Castaneda, L.J. / Napuli, A.J. / Zhang, Z. / Fan, E. / Zucker, F.H. / Verlinde, C.L. / Buckner, F.S. / Van Voorhis, W.C. / Hol, W.G. / Merritt, E.A.
History
DepositionSep 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms ..._chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosyl-tRNA synthetase
B: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,4494
Polymers154,1142
Non-polymers3342
Water0
1
A: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2242
Polymers77,0571
Non-polymers1671
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2242
Polymers77,0571
Non-polymers1671
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)241.400, 241.400, 241.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A0 - 363
2112B0 - 363
1122A365 - 682
2122B365 - 682

NCS ensembles :
ID
1
2

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Components

#1: Protein Tyrosyl-tRNA synthetase


Mass: 77057.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LmjF14.1370 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4QFJ7, tyrosine-tRNA ligase
#2: Chemical ChemComp-TYE / 4-[(2S)-2-amino-3-hydroxypropyl]phenol / tyrosinol / bound form of TYROSINAL / Tyrosinol


Type: L-peptide linking / Mass: 167.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13NO2

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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: 3.8 Å3/Da / Density % sol: 67.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: equal volumes SeMet protein solution (24 mg/ml LmTyrRS in MSGPP buffer containing 5 mM DTT and 10 mM tyrosinol) and well solution (25% PEG 3350, 0.1 M tri-sodium citrate pH 5.5, 10 mM Ferric ...Details: equal volumes SeMet protein solution (24 mg/ml LmTyrRS in MSGPP buffer containing 5 mM DTT and 10 mM tyrosinol) and well solution (25% PEG 3350, 0.1 M tri-sodium citrate pH 5.5, 10 mM Ferric III Chloride); cryoprotected by addition of 26% PEG 3350, 8% MSGPP buffer, 8% ethylene glycol, 20% glycerol and 0.09 M tri-sodium citrate pH 5.5 directly to drop prior to mounting and freezing crystals in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97908 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2010
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 3.13→85.35 Å / Num. obs: 41253 / % possible obs: 99.93 % / Redundancy: 7.98 % / Biso Wilson estimate: 83 Å2 / Rmerge(I) obs: 0.182 / Net I/σ(I): 7.3331
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.13-3.36.960.014199.82
3.3-3.57.340.014199.92
3.5-3.747.590.014199.91
3.74-4.047.860.014199.95
4.04-4.428.360.0141100
4.42-4.958.750.0141100
4.95-5.718.790.0141100
5.71-78.760.0141100
7-9.898.670.0141100
9.89-85.358.260.014199.52

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALACCP4_3.3.16data scaling
REFMACrefmac_5.5.0110refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3P0H

3p0h


Resolution: 3.13→85.35 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.898 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 48.246 / SU ML: 0.369 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 2062 5 %RANDOM
Rwork0.2395 ---
obs0.2409 41212 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 122.862 Å2
Refinement stepCycle: LAST / Resolution: 3.13→85.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9278 0 24 0 9302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229476
X-RAY DIFFRACTIONr_bond_other_d0.0020.026315
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.96412845
X-RAY DIFFRACTIONr_angle_other_deg0.925315432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94551207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92124.458406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.697151637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7181558
X-RAY DIFFRACTIONr_chiral_restr0.0650.21479
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021819
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
12105TIGHT POSITIONAL0.020.05
12581MEDIUM POSITIONAL0.030.5
21056TIGHT POSITIONAL0.020.05
21148MEDIUM POSITIONAL0.020.5
LS refinement shellResolution: 3.13→3.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 165 -
Rwork0.35 2833 -
all-2998 -
obs--99.54 %
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)
16.38832.20071.80772.3293-0.2331.31810.0694-0.4957-0.48640.4547-0.1708-0.19570.0503-0.04940.10150.31930.13650.16060.25530.16590.531922.41267.37764.14
28.44222.8698-2.54242.9094-0.54552.66280.18040.28170.03910.0944-0.10360.63080.3889-0.3141-0.07680.4477-0.05320.12950.29390.07150.8158-24.44646.38169.548
32.8995-1.4522-0.82687.03251.62051.6380.00460.54590.2811-0.4573-0.0070.0338-0.349-0.19080.00240.19960.13650.05630.35360.11480.50823.72892.32841.417
416.2024-3.7914-11.34823.82363.508411.04220.59513.5367-0.4229-0.578-0.90890.4050.2049-2.41850.31380.46360.15160.01831.4473-0.18510.642719.9869.50210.545
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 364
2X-RAY DIFFRACTION1A701
3X-RAY DIFFRACTION2A365 - 680
4X-RAY DIFFRACTION3B-1 - 355
5X-RAY DIFFRACTION3B701
6X-RAY DIFFRACTION4B366 - 544

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