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- PDB-4yrs: Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex... -

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Basic information

Entry
Database: PDB / ID: 4yrs
TitleCrystal structure of T. cruzi Histidyl-tRNA synthetase in complex with N-(quinolin-3-yl)propanamide (Chem 1698)
ComponentsHistidyl-tRNA synthetase
KeywordsLigase/Ligase inhibitor / ligase / aminoacyl-tRNA synthetase / aaRS / HisRS / Trypanosoma cruzi / protein-inhibitor complex / Ligase-Ligase inhibitor complex
Function / homology
Function and homology information


histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / 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) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-(quinolin-3-yl)propanamide / HISTIDINE / histidine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKoh, C.-Y. / Hol, W.G.J.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens.
Authors: Koh, C.Y. / Siddaramaiah, L.K. / Ranade, R.M. / Nguyen, J. / Jian, T. / Zhang, Z. / Gillespie, J.R. / Buckner, F.S. / Verlinde, C.L. / Fan, E. / Hol, W.G.
History
DepositionMar 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5423
Polymers51,1861
Non-polymers3562
Water54030
1
A: Histidyl-tRNA synthetase
hetero molecules

A: Histidyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0846
Polymers102,3712
Non-polymers7134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area7360 Å2
ΔGint-30 kcal/mol
Surface area34210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.455, 119.677, 66.750
Angle α, β, γ (deg.)90.000, 94.170, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Histidyl-tRNA synthetase


Mass: 51185.590 Da / Num. of mol.: 1 / Fragment: UNP residues 45-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / Gene: Tc00.1047053507019.40 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4DA54, histidine-tRNA ligase
#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical ChemComp-4JS / N-(quinolin-3-yl)propanamide / N-(quinolin-3-yl)prop-2-enamide, bound form


Mass: 200.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE 4JS LIGAND IS ATTACHED TO SG ATOM OF CYS A 365 TO FORM A COVALENT LINKAGE. THE LIGAND 4JS ...THE 4JS LIGAND IS ATTACHED TO SG ATOM OF CYS A 365 TO FORM A COVALENT LINKAGE. THE LIGAND 4JS REPRESENTS THE FINAL BOUND PRODUCT. THE STARTING MATERIAL FOR 4JS LIGAND HASA DOUBLE BOND BETWEEN C AND C1 ATOM GROUPS.

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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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 23 % to 28 % PEG 3350, 0.1 M sodium citrate pH 4.8 to 5.3, 1 mM TCEP
PH range: 4.8 to 5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2014
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.75→37.81 Å / Num. obs: 13023 / % possible obs: 96.2 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.03 / Net I/σ(I): 17 / Num. measured all: 53548
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.75-2.94.20.7292817319380.7320.40297.6
8.7-37.813.90.01757.415644040.9990.0190.5

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
REFMACrefmac_5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LC0

3lc0


Resolution: 2.75→37.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.918 / SU B: 28.9 / SU ML: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 657 5 %RANDOM
Rwork0.1807 ---
obs0.1834 12361 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 159.86 Å2 / Biso mean: 78.757 Å2 / Biso min: 22.87 Å2
Baniso -1Baniso -2Baniso -3
1-4.24 Å2-0 Å2-2.29 Å2
2---0.53 Å2-0 Å2
3----3.34 Å2
Refinement stepCycle: final / Resolution: 2.75→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 26 30 3290
Biso mean--67.3 58.61 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193333
X-RAY DIFFRACTIONr_bond_other_d0.0010.023182
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.9684526
X-RAY DIFFRACTIONr_angle_other_deg0.71637278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5275417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59522.857147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37915537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.721530
X-RAY DIFFRACTIONr_chiral_restr0.0570.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02771
X-RAY DIFFRACTIONr_mcbond_it1.4774.31674
X-RAY DIFFRACTIONr_mcbond_other1.4774.3011675
X-RAY DIFFRACTIONr_mcangle_it2.4976.4442087
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 51 -
Rwork0.326 897 -
all-948 -
obs--97.03 %
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)
15.2173-0.143-1.21021.93960.18722.91510.22020.15830.8912-0.1021-0.05410.011-0.69780.0026-0.16610.219-0.00010.08940.17410.04860.23670.1442.70325.73
21.87352.6578-0.27957.2308-0.30231.9916-0.15010.53930.5851-0.77810.2115-0.1118-0.83750.3243-0.06140.5268-0.10320.10730.73820.18280.515982.9336.4052.441
33.08280.733-1.43750.939-0.74062.14110.00860.370.0155-0.09910.06080.1157-0.0925-0.2427-0.06940.06940.02290.06890.167-0.03590.212861.31-9.64324.869
46.8543-0.5877-1.72956.4265-0.530414.1904-0.02890.1069-0.7481-0.13030.15710.36111.0256-0.699-0.12820.393-0.12710.01090.3493-0.00040.753139.599-31.57744.246
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A47 - 197
2X-RAY DIFFRACTION2A198 - 292
3X-RAY DIFFRACTION3A293 - 438
4X-RAY DIFFRACTION4A439 - 478

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