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

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Basic information

Entry
Database: PDB / ID: 4ypf
TitleCrystal structure of T. cruzi Histidyl-tRNA synthetase in complex with quinolin-3-amine (Chem 84)
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
quinolin-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 12, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9929
Polymers51,1861
Non-polymers8078
Water1,71195
1
A: Histidyl-tRNA synthetase
hetero molecules

A: Histidyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,98518
Polymers102,3712
Non-polymers1,61416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area10220 Å2
ΔGint-124 kcal/mol
Surface area32950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.665, 119.140, 66.100
Angle α, β, γ (deg.)90.000, 92.550, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-505-

SO4

21A-681-

HOH

31A-691-

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 , 6 types, 103 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-4FS / quinolin-3-amine


Mass: 144.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 50.5 %
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: Feb 28, 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 Å / Num. obs: 24924 / % possible obs: 98.4 % / Redundancy: 2.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.041 / Net I/σ(I): 15.1 / Num. measured all: 72379
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
2.2-2.272.50.5811.8487519660.740.43290.2
9.07-362.90.01576.69763370.9990.01189.1

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Processing

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

3lc0


Resolution: 2.2→36 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.573 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 1303 5.2 %RANDOM
Rwork0.2006 ---
obs0.2027 23616 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.27 Å2 / Biso mean: 54.029 Å2 / Biso min: 22.39 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å20 Å2-0.67 Å2
2--3.18 Å20 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 2.2→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 49 95 3252
Biso mean--51.67 40.86 -
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193231
X-RAY DIFFRACTIONr_bond_other_d0.0010.023046
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.9614383
X-RAY DIFFRACTIONr_angle_other_deg0.74136951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4715405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19622.695141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63915506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3161529
X-RAY DIFFRACTIONr_chiral_restr0.0590.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213708
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02753
X-RAY DIFFRACTIONr_mcbond_it0.6451.9631627
X-RAY DIFFRACTIONr_mcbond_other0.6461.9631627
X-RAY DIFFRACTIONr_mcangle_it1.0892.9322023
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 89 -
Rwork0.288 1543 -
all-1632 -
obs--88.65 %
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)
14.1918-0.1352-0.66410.97610.20234.51360.14820.52180.65780.05440.05720.0024-0.58160.1885-0.20530.2465-0.01940.08760.08610.07480.121270.662.06622.866
22.025-0.5114-0.27779.6976-3.05155.44460.26391.21330.605-0.5765-0.1623-0.0042-0.6671.0963-0.10160.4127-0.10010.08231.19340.29570.262482.3013.8732.082
34.15430.97081.03311.46550.56995.61960.06760.75370.4314-0.0410.04180.1559-0.29370.0877-0.10950.20620.0150.07380.1560.07280.074472.072-1.10113.316
48.25251.2259-1.60273.28520.70534.36720.0196-0.1473-1.0573-0.0625-0.07730.29480.6868-0.60060.05780.3895-0.13530.00940.15160.13410.392440.727-23.58242.95
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 221
2X-RAY DIFFRACTION2A222 - 302
3X-RAY DIFFRACTION3A303 - 379
4X-RAY DIFFRACTION4A380 - 478

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