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

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Basic information

Entry
Database: PDB / ID: 4yrt
TitleCrystal structure of T. cruzi Histidyl-tRNA synthetase in complex with N-(5-hydroxynaphthalen-2-yl)propanamide (Chem 1781)
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-(5-hydroxynaphthalen-2-yl)propanamide / HISTIDINE / histidine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly / pdbx_struct_oper_list
Item: _chem_comp.name / _citation.journal_abbrev ..._chem_comp.name / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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 / diffrn_radiation_wavelength / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Oct 23, 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)51,7155
Polymers51,1861
Non-polymers5304
Water3,909217
1
A: Histidyl-tRNA synthetase
hetero molecules

A: Histidyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,43010
Polymers102,3712
Non-polymers1,0598
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area8480 Å2
ΔGint-66 kcal/mol
Surface area33260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.432, 119.340, 66.302
Angle α, β, γ (deg.)90.000, 93.390, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

21A-787-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 221 molecules

#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-781 / N-(5-hydroxynaphthalen-2-yl)propanamide / N-(5-hydroxynaphthalen-2-yl)prop-2-enamide, bound form


Mass: 215.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13NO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHE 781 LIGAND IS ATTACHED TO SG ATOM OF CYS A 365 TO FORM A COVALENT LINKAGE. THE LIGAND 781 ...THE 781 LIGAND IS ATTACHED TO SG ATOM OF CYS A 365 TO FORM A COVALENT LINKAGE. THE LIGAND 781 REPRESENTS THE FINAL BOUND PRODUCT. THE STARTING MATERIAL FOR 781 LIGAND IS N-(5-HYDROXYNAPHTHALEN-2-YL)PROP-2-ENAMIDE WHICH HAS A DOUBLE BOND BETWEEN C8 AND C9 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: 2.52 Å3/Da / Density % sol: 51.27 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 21, 2014
RadiationMonochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→29.09 Å / Num. obs: 31152 / % possible obs: 98 % / Redundancy: 2.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.041 / Net I/σ(I): 15.6 / Num. measured all: 79897
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
2.05-2.112.10.4611.9453321710.740.36887.7
8.94-37.372.50.01177.692436610.00991.6

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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: 2.05→29.09 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.462 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 1597 5.1 %RANDOM
Rwork0.1853 ---
obs0.1874 29548 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.49 Å2 / Biso mean: 38.198 Å2 / Biso min: 17.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å2-1.14 Å2
2---0.49 Å20 Å2
3----0.85 Å2
Refinement stepCycle: final / Resolution: 2.05→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 0 36 217 3454
Biso mean--32.35 36.55 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193324
X-RAY DIFFRACTIONr_bond_other_d0.0010.023175
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.9724518
X-RAY DIFFRACTIONr_angle_other_deg0.73937271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4155419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77523.034145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18215537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4891528
X-RAY DIFFRACTIONr_chiral_restr0.0610.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213742
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02761
X-RAY DIFFRACTIONr_mcbond_it0.6941.9891665
X-RAY DIFFRACTIONr_mcbond_other0.6941.9891663
X-RAY DIFFRACTIONr_mcangle_it1.1362.9752075
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 95 -
Rwork0.254 1946 -
all-2041 -
obs--87.11 %
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)
12.1848-0.1006-0.51881.21990.23562.23740.09870.13990.3593-0.03270.01-0.0716-0.52030.0979-0.10870.1216-0.02440.02080.01710.02140.061772.0563.16121.829
20.365-1.86660.817913.2561-2.78652.6530.02140.22750.134-0.9423-0.3211-0.2085-0.54630.6950.29960.458-0.0950.09790.5780.14250.313382.687.456-0.963
32.28780.620.27281.66410.17652.1580.07640.30350.1539-0.0318-0.0509-0.0153-0.15660.0185-0.02550.01840.01220.01130.05870.02350.01474.428-2.81913.002
44.08310.6865-0.69493.4326-0.34865.41660.0803-0.0128-0.4268-0.1268-0.05130.29040.3894-0.3745-0.02890.0409-0.0335-0.03060.0440.02050.160940.605-23.50443.023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 238
2X-RAY DIFFRACTION2A239 - 291
3X-RAY DIFFRACTION3A292 - 379
4X-RAY DIFFRACTION4A380 - 478

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