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- PDB-5usf: Leishmania donovani tyrosyl-tRNA synthetase in complex with nanob... -

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Basic information

Entry
Database: PDB / ID: 5usf
TitleLeishmania donovani tyrosyl-tRNA synthetase in complex with nanobody and inhibitor
Components
  • Immunoglobulin heavy chain variable region
  • Tyrosyl-tRNA synthetase, putative
Keywordsligase/ligase inhibitor / synthetase / ligase / tyrosine / inhibitor / Ligase-Ligase Inhibitor complex / tyrosyl-adenylate analog
Function / homology
Function and homology information


aminoacyl-tRNA ligase activity / tRNA aminoacylation for protein translation / ATP binding
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / Tyrosyl-tRNA synthetase, putative
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBarros-Alvarez, X. / Hol, W.G.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1 AI084004 and RO1 AI097177 United States
CitationJournal: Biochimie / Year: 2017
Title: Leishmania donovani tyrosyl-tRNA synthetase structure in complex with a tyrosyl adenylate analog and comparisons with human and protozoan counterparts.
Authors: Barros-Alvarez, X. / Kerchner, K.M. / Koh, C.Y. / Turley, S. / Pardon, E. / Steyaert, J. / Ranade, R.M. / Gillespie, J.R. / Zhang, Z. / Verlinde, C.L.M.J. / Fan, E. / Buckner, F.S. / Hol, W.G.J.
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosyl-tRNA synthetase, putative
B: Tyrosyl-tRNA synthetase, putative
C: Immunoglobulin heavy chain variable region
D: Immunoglobulin heavy chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,1236
Polymers179,1044
Non-polymers1,0192
Water6,359353
1
A: Tyrosyl-tRNA synthetase, putative
D: Immunoglobulin heavy chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0623
Polymers89,5522
Non-polymers5091
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-7 kcal/mol
Surface area33270 Å2
MethodPISA
2
B: Tyrosyl-tRNA synthetase, putative
C: Immunoglobulin heavy chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0623
Polymers89,5522
Non-polymers5091
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-9 kcal/mol
Surface area32950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.180, 96.180, 351.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYSAA-1 - 6803 - 684
21GLYGLYLYSLYSBB-1 - 6803 - 684
12GLNGLNSERSERCC1 - 1171 - 117
22GLNGLNSERSERDD1 - 1171 - 117

NCS ensembles :
ID
1
2

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Components

#1: Protein Tyrosyl-tRNA synthetase, putative


Mass: 75341.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (strain BPK282A1) (eukaryote)
Strain: BPK282A1 / Gene: LDBPK_141460 / Production host: Escherichia coli (E. coli) / References: UniProt: E9BC28
#2: Antibody Immunoglobulin heavy chain variable region


Mass: 14210.714 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-YSA / 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / TYROSYLADENYLATE


Mass: 509.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O8S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 0.1 M sodium cacodylate pH 5.7, 22% PEG 4,000, vapor diffusion, sitting drop, temperature 298

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2015
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.75→83.29 Å / Num. obs: 47547 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.21 / Net I/σ(I): 8.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimlessdata scaling
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P0J

3p0j


Resolution: 2.75→83.29 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: THROUGHOUT / ESU R Free: 0.361 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24353 2311 4.9 %RANDOM
Rwork0.18886 ---
obs0.19144 45156 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å2-0 Å2
2---0.22 Å20 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 2.75→83.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12283 0 70 353 12706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912576
X-RAY DIFFRACTIONr_bond_other_d00.0212099
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9617044
X-RAY DIFFRACTIONr_angle_other_deg3.75327800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66651595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84924.307548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.213152161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1691586
X-RAY DIFFRACTIONr_chiral_restr0.0830.21932
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214497
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022789
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_it3.6766.4196397
X-RAY DIFFRACTIONr_mcbond_other3.6766.4196398
X-RAY DIFFRACTIONr_mcangle_it5.819.6257985
X-RAY DIFFRACTIONr_mcangle_other5.8099.6247986
X-RAY DIFFRACTIONr_scbond_it3.8696.6776179
X-RAY DIFFRACTIONr_scbond_other3.8686.6776180
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3089.8539060
X-RAY DIFFRACTIONr_long_range_B_refined9.33849.32113861
X-RAY DIFFRACTIONr_long_range_B_other9.33849.32113862
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A793000.11
12B793000.11
21C136940.06
22D136940.06
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 141 -
Rwork0.298 3350 -
obs--99.43 %

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