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- PDB-3vgj: Crystal of Plasmodium falciparum tyrosyl-tRNA synthetase (PfTyrRS... -

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Basic information

Entry
Database: PDB / ID: 3vgj
TitleCrystal of Plasmodium falciparum tyrosyl-tRNA synthetase (PfTyrRS)in complex with adenylate analog
ComponentsTyrosyl-tRNA synthetase, putative
KeywordsLIGASE / TyrRS / Synthetase
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / host cell cytosol / host cell surface receptor binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, archaeal/eukaryotic-type / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Tyrosine-tRNA ligase, archaeal/eukaryotic-type / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / TYROSINE / tyrosine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.212 Å
AuthorsBanday, M.M. / Yogavel, M. / Bhatt, T.K. / Khan, S. / Sharma, A. / Sharma, A.
CitationJournal: Nat Commun / Year: 2011
Title: Malaria parasite tyrosyl-tRNA synthetase secretion triggers pro-inflammatory responses.
Authors: Bhatt, T.K. / Khan, S. / Dwivedi, V.P. / Banday, M.M. / Sharma, A. / Chandele, A. / Camacho, N. / de Pouplana, L.R. / Wu, Y. / Craig, A.G. / Mikkonen, A.T. / Maier, A.G. / Yogavel, M. / Sharma, A.
History
DepositionAug 14, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Non-polymer description
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosyl-tRNA synthetase, putative
B: Tyrosyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0856
Polymers87,0282
Non-polymers1,0574
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-21 kcal/mol
Surface area29920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.560, 46.500, 141.350
Angle α, β, γ (deg.)90.00, 93.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tyrosyl-tRNA synthetase, putative


Mass: 43514.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: MAL8P1.125 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IAR7, tyrosine-tRNA ligase
#2: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.59 Å3/Da / Density % sol: 52.54 % / Mosaicity: 0.699 °
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10mM MgCl2, 10mM ATP, 2mM L-Tyrosine, 2.4mM sodium malonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 4, 2009 / Details: mirros
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. all: 45469 / Num. obs: 43059 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Redundancy: 14.1 % / Rmerge(I) obs: 0.056 / Χ2: 1.224 / Net I/σ(I): 17.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.21-2.299.80.40536721.052182.2
2.29-2.3812.90.40342180.975194
2.38-2.4914.30.30942830.991194.5
2.49-2.62150.24442801.016194.9
2.62-2.7815.10.16243291.089195.6
2.78-315.10.10843321.305195.9
3-3.3150.07344081.365196.5
3.3-3.7814.90.05244211.645197.1
3.78-4.7614.60.0444781.328197.7
4.76-50140.03946381.331197.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
DENZOdata reduction
HKL-2000data scaling
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.212→40.025 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 2000 4.67 %
Rwork0.1719 --
obs0.1739 42842 94.91 %
all-45144 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.729 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 236.64 Å2 / Biso mean: 56.4394 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.7832 Å2-0 Å22.6573 Å2
2--2.8998 Å20 Å2
3----1.1167 Å2
Refinement stepCycle: LAST / Resolution: 2.212→40.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5701 0 70 331 6102
LS refinement shellResolution: 2.214→2.2677 Å
RfactorNum. reflection
Rfree0.3335 111
Rwork0.2427 -
obs-2533
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)
1-0.1646-0.3262-0.05310.85190.12280.2730.3757-0.49970.21810.05260.4156-1.14430.35260.5213-0.51320.54730.22650.10670.7986-0.47830.993230.9785-6.660346.2555
21.2486-0.10250.99840.40440.00091.88540.036-0.0452-0.0917-0.02050.10930.05-0.0457-0.0173-0.10340.31020.06810.02990.32320.00230.30169.682-0.668949.0685
30.9058-0.04250.27250.9064-0.6031.7138-0.0103-0.2316-0.0410.20330.03370.10590.1146-0.4595-0.01550.3183-0.0040.02580.4752-0.02410.268717.058-4.93174.3592
40.1292-0.08320.09961.57440.1110.40250.38880.05930.2737-0.3562-0.23210.8584-0.1135-0.8396-0.17110.52850.22580.22320.74920.08010.7575-34.936313.085729.3853
51.5792-0.15960.83780.7187-0.17932.0498-0.0203-0.1314-0.00790.10990.082-0.073-0.1055-0.1137-0.05020.31970.03920.01910.295-0.03020.3432-13.02494.222827.6698
61.49-0.08210.94322.90720.02760.81430.10990.1499-0.2869-0.40740.07970.66590.17870.0352-0.16940.3402-0.0034-0.09180.2228-0.01390.4551-25.5479-2.45294.3372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 20:56)A20 - 56
2X-RAY DIFFRACTION2(CHAIN A AND RESID 57:245)A57 - 245
3X-RAY DIFFRACTION3(CHAIN A AND RESID 246:369)A246 - 369
4X-RAY DIFFRACTION4(CHAIN B AND RESID 18:55)B18 - 55
5X-RAY DIFFRACTION5(CHAIN B AND RESID 56:237)B56 - 237
6X-RAY DIFFRACTION6(CHAIN B AND RESID 238:369)B238 - 369

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