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

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Basic information

Entry
Database: PDB / ID: 4yrk
TitleCrystal structure of T. cruzi Histidyl-tRNA synthetase in complex with (4-chlorophenyl)methanol (Chem 260)
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
(4-chlorophenyl)methanol / 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)103,88617
Polymers102,3712
Non-polymers1,51415
Water5,242291
1
A: Histidyl-tRNA synthetase
hetero molecules

B: Histidyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,88617
Polymers102,3712
Non-polymers1,51415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area10040 Å2
ΔGint-105 kcal/mol
Surface area33560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.910, 118.736, 93.705
Angle α, β, γ (deg.)90.000, 91.450, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-691-

HOH

21B-709-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histidyl-tRNA synthetase


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, 306 molecules

#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical ChemComp-4JL / (4-chlorophenyl)methanol


Mass: 142.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7ClO
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
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→35.83 Å / Num. obs: 48253 / % possible obs: 96.9 % / Redundancy: 2.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.07 / Net I/σ(I): 9.7 / Num. measured all: 136941
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
2.2-2.272.10.5521.6697133350.6710.42777.7
9.07-35.832.90.02236.919616880.9990.01693.5

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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→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.335 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 2450 5.1 %RANDOM
Rwork0.1993 ---
obs0.2007 45798 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.87 Å2 / Biso mean: 35.539 Å2 / Biso min: 12.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0 Å20.19 Å2
2--1.08 Å20 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6415 0 89 291 6795
Biso mean--39.23 31.47 -
Num. residues----822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196647
X-RAY DIFFRACTIONr_bond_other_d0.0020.026378
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9669003
X-RAY DIFFRACTIONr_angle_other_deg0.776314603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3895826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87522.795297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.133151100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4671562
X-RAY DIFFRACTIONr_chiral_restr0.0580.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217510
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021532
X-RAY DIFFRACTIONr_mcbond_it0.7111.8083300
X-RAY DIFFRACTIONr_mcbond_other0.7091.8073297
X-RAY DIFFRACTIONr_mcangle_it1.2412.6994108
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 153 -
Rwork0.29 2649 -
all-2802 -
obs--76.24 %
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)
11.32280.03290.20890.97940.41153.41180.042-0.1106-0.30650.14290.03550.01980.5107-0.2176-0.07750.0836-0.0279-0.01140.02530.02940.072319.0532-2.643737.8982
21.855-1.4372-3.66345.75064.30927.7018-0.1609-0.1364-0.17780.3736-0.21930.24130.3810.16760.38020.5107-0.0697-0.0160.36970.14190.45287.9063-18.442658.9835
32.4725-0.88640.08981.9726-0.39752.7987-0.0194-0.3489-0.1290.21220.05490.14520.1727-0.5299-0.03550.0525-0.04940.02230.15670.01520.02313.19973.004649.6898
43.2213-0.15330.04543.6096-0.25176.5631-0.0570.02420.3694-0.09170.0940.4-0.563-0.4731-0.0370.15670.0412-0.03730.05780.06080.195613.929822.8372-0.296
51.35150.03780.28861.25140.40013.578-0.0115-0.0861-0.2430.11690.05010.03120.5111-0.0734-0.03860.0781-0.00440.00580.00920.0170.044918.183355.756484.303
613.965-0.632-12.61082.67391.064911.4824-0.6909-0.135-0.64570.25480.02790.40050.710.13360.6630.8135-0.10480.0660.39350.00840.46847.832238.4374104.2484
72.4765-0.75780.21622.14540.02222.8228-0.0234-0.3068-0.0620.25850.00970.17470.2513-0.42570.01370.0577-0.04520.0270.0999-0.00490.021112.207760.44796.2657
84.6751-0.0808-0.02932.479-0.29725.7859-0.01490.11720.3878-0.1120.01830.2771-0.7238-0.1807-0.00340.19450.0129-0.01930.0230.03140.09512.273883.396547.7401
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 239
2X-RAY DIFFRACTION2A244 - 260
3X-RAY DIFFRACTION3A261 - 379
4X-RAY DIFFRACTION4A380 - 478
5X-RAY DIFFRACTION5B48 - 240
6X-RAY DIFFRACTION6B245 - 260
7X-RAY DIFFRACTION7B261 - 379
8X-RAY DIFFRACTION8B380 - 478

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