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

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Basic information

Entry
Database: PDB / ID: 4yrn
TitleCrystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 6-bromopyridin-3-amine (Chem 475)
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-bromopyridin-3-amine / HISTIDINE / histidine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,21121
Polymers102,3712
Non-polymers1,84019
Water8,143452
1
B: Histidyl-tRNA synthetase
hetero molecules

A: Histidyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,21121
Polymers102,3712
Non-polymers1,84019
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area10670 Å2
ΔGint-92 kcal/mol
Surface area34000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.245, 119.221, 94.232
Angle α, β, γ (deg.)90.000, 91.280, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-754-

HOH

21A-791-

HOH

31B-761-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 51185.590 Da / Num. of mol.: 2 / 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, 471 molecules

#2: Chemical ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical ChemComp-4JN / 6-bromopyridin-3-amine


Mass: 173.011 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5BrN2
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
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: Jan 9, 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: 2.2→36.37 Å / Num. obs: 49893 / % possible obs: 98.8 % / Redundancy: 2.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.072 / Net I/σ(I): 9.3 / Num. measured all: 143911
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
2.2-2.272.40.5791.7989541150.6720.42794.8
9.07-36.372.80.01937.320007080.9990.01394.3

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Processing

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

3lc0


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 12.198 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.275 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 2503 5 %RANDOM
Rwork0.2051 ---
obs0.2068 47387 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.01 Å2 / Biso mean: 37.619 Å2 / Biso min: 10.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20.52 Å2
2--1.09 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6396 0 103 452 6951
Biso mean--37.42 32.85 -
Num. residues----829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196627
X-RAY DIFFRACTIONr_bond_other_d0.0020.026311
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.9658976
X-RAY DIFFRACTIONr_angle_other_deg0.782314433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3465826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5322.941289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4031557
X-RAY DIFFRACTIONr_chiral_restr0.060.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217496
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021517
X-RAY DIFFRACTIONr_mcbond_it0.4881.4013321
X-RAY DIFFRACTIONr_mcbond_other0.4881.4013322
X-RAY DIFFRACTIONr_mcangle_it0.8612.0924131
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 180 -
Rwork0.296 3276 -
all-3456 -
obs--93.73 %
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)
12.65010.71280.94431.79280.77414.0640.1694-0.0405-0.47820.16680.0332-0.06260.6345-0.1093-0.20260.1004-0.0156-0.03360.00570.01080.089821.754-4.34531.553
22.6446-0.32810.17570.3814-0.68615.1869-0.0301-0.2899-0.10330.06730.030.00580.4188-0.58040.00010.0888-0.0778-0.0010.11570.01220.004215.132.88342.973
32.9455-0.53050.51129.7556-3.595517.8564-0.2397-0.4206-0.39740.26310.42310.63280.9705-1.2459-0.18340.5732-0.14320.03590.27040.170.38412.337-14.35156.569
43.3073-0.94410.30851.9787-0.35823.1643-0.0376-0.5026-0.2030.24470.08510.16130.2838-0.527-0.04750.0795-0.053-0.00220.19570.03780.044213.4441.89550.711
54.3809-1.2957-0.19374.1013-0.37478.7817-0.07570.22840.6507-0.22420.02990.3142-0.8282-0.63010.04580.20650.0389-0.10060.09280.10160.286514.24423.121-0.32
62.79640.5371.11642.12570.36884.10610.09220.0183-0.39120.07330.0615-0.01330.58050.0528-0.15370.08440.0078-0.01160.0052-0.00050.056621.02754.97678.177
72.8589-0.99230.61071.2244-0.11515.12360.0758-0.28280.0184-0.0294-0.10940.13260.3895-0.49490.03360.0301-0.03780.00120.1105-0.03570.022114.00161.65188.746
82.3920.8621-3.4298.68482.3869.8696-0.0338-0.6489-0.51311.0373-0.45590.551.7203-0.69680.48970.7482-0.4712-0.0990.92510.34260.347410.75547.699106.783
93.7267-0.761-0.20241.8138-0.02342.9950.0279-0.26080.02170.099-0.02190.03880.1959-0.4618-0.00590.032-0.0399-0.00740.0986-0.00220.0113.68961.97493.813
106.02980.1615-0.02233.258-0.94567.90250.00030.25070.6111-0.10610.03820.2924-0.8534-0.3633-0.03850.2050.0271-0.05960.04070.06530.200212.68883.7347.724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 156
2X-RAY DIFFRACTION2A157 - 218
3X-RAY DIFFRACTION3A219 - 253
4X-RAY DIFFRACTION4A254 - 379
5X-RAY DIFFRACTION5A380 - 478
6X-RAY DIFFRACTION6B48 - 155
7X-RAY DIFFRACTION7B156 - 215
8X-RAY DIFFRACTION8B216 - 282
9X-RAY DIFFRACTION9B283 - 379
10X-RAY DIFFRACTION10B380 - 478

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