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

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Basic information

Entry
Database: PDB / ID: 4yrq
TitleCrystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 6-amino-2H-chromen-2-one (Chem 744)
ComponentsHistidyl-tRNA synthetaseHistidine—tRNA ligase
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
6-amino-2H-chromen-2-one / 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 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Apr 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
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
Revision 1.3Sep 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 / 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

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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)51,8177
Polymers51,1861
Non-polymers6326
Water3,657203
1
A: Histidyl-tRNA synthetase
hetero molecules

A: Histidyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,63514
Polymers102,3712
Non-polymers1,26312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area9180 Å2
ΔGint-64 kcal/mol
Surface area33710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.097, 119.271, 66.140
Angle α, β, γ (deg.)90.000, 92.850, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-769-

HOH

21A-771-

HOH

31A-790-

HOH

41A-795-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histidyl-tRNA synthetase / Histidine—tRNA ligase


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 , 6 types, 209 molecules

#2: Chemical ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical ChemComp-4JQ / 6-amino-2H-chromen-2-one


Mass: 161.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
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: May 20, 2013
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→27.82 Å / Num. obs: 31011 / % possible obs: 98.2 % / Redundancy: 2.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.037 / Net I/σ(I): 10.6 / Num. measured all: 87563
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.05-2.1120.3362.4447021860.7990.2789.6
8.94-27.8230.01930.710693550.9990.01388.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
Aimless0.1.27data scaling
REFMACrefmac_5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LC0

3lc0


Resolution: 2.05→27.82 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.604 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 1590 5.1 %RANDOM
Rwork0.1843 ---
obs0.186 29417 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.36 Å2 / Biso mean: 39.798 Å2 / Biso min: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å2-0 Å20.77 Å2
2---0.42 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 2.05→27.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 0 40 203 3415
Biso mean--42.13 39.52 -
Num. residues----412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193283
X-RAY DIFFRACTIONr_bond_other_d0.0010.023147
X-RAY DIFFRACTIONr_angle_refined_deg1.0861.9614451
X-RAY DIFFRACTIONr_angle_other_deg0.72137192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3495412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8622.59139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46515528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3251529
X-RAY DIFFRACTIONr_chiral_restr0.0560.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213753
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02760
X-RAY DIFFRACTIONr_mcbond_it0.9882.2321652
X-RAY DIFFRACTIONr_mcbond_other0.9872.2341653
X-RAY DIFFRACTIONr_mcangle_it1.7013.3312056
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 98 -
Rwork0.242 1962 -
all-2060 -
obs--88.91 %
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)
10.5517-0.0164-0.39510.02790.00520.71650.05420.07140.01470.01350.05350.0044-0.20290.031-0.10770.1674-0.007-0.01630.13690.00920.144668.5014.74826.878
20.47970.0080.35050.1196-0.43191.96050.080.348-0.14770.0762-0.0394-0.0082-0.16270.4283-0.04060.1056-0.0062-0.0250.343-0.05880.093979.361-0.57410.485
30.9435-3.4061-0.103814.1856-1.32664.24580.21660.1975-0.1918-0.8658-0.46040.9672-0.61931.20490.24370.2328-0.3181-0.16380.86150.25370.165681.5568.549-1.768
40.82170.20980.30840.2253-0.02591.40920.09810.24530.0428-0.0062-0.03610.022-0.13920.0836-0.06210.09210.0133-0.02240.2196-0.00220.101574.735-3.17612.246
52.07750.3683-0.1220.8102-0.09270.98060.0729-0.0514-0.2293-0.04460.02370.11480.1353-0.0803-0.09660.0747-0.0583-0.06890.12620.07160.205140.95-23.63442.961
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 173
2X-RAY DIFFRACTION2A174 - 237
3X-RAY DIFFRACTION3A238 - 286
4X-RAY DIFFRACTION4A287 - 379
5X-RAY DIFFRACTION5A380 - 478

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