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- PDB-9ys2: Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasm... -

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Basic information

Entry
Database: PDB / ID: 9ys2
TitleCrystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with cysteinyl-AMP
ComponentsCysteine--tRNA ligase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Cysteinyl-tRNA synthetase / CysRS
Function / homology
Function and homology information


cysteine-tRNA ligase / cysteine-tRNA ligase activity / cysteinyl-tRNA aminoacylation / apicoplast / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Cysteine-tRNA ligase / Cysteinyl-tRNA synthetase/mycothiol ligase / tRNA synthetases class I, catalytic domain / tRNA synthetases class I (C) catalytic domain / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
: / ADENOSINE-5'-TRIPHOSPHATE / MALONATE ION / cysteine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with cysteinyl-AMP
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionOct 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine--tRNA ligase
B: Cysteine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,71417
Polymers109,0662
Non-polymers2,64815
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-98 kcal/mol
Surface area33360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.044, 120.044, 365.723
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-719-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cysteine--tRNA ligase / Cysteinyl-tRNA synthetase


Mass: 54533.195 Da / Num. of mol.: 2 / Fragment: residues 91-535
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1015200.1 / Plasmid: PlfaA.00133.a.A3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IJP3, cysteine-tRNA ligase

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Non-polymers , 6 types, 270 molecules

#2: Chemical ChemComp-A1CYZ / 5'-O-[(R)-{[(2R)-2-amino-3-sulfanylpropanoyl]oxy}(hydroxy)phosphoryl]adenosine


Mass: 450.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N6O8PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.49 Å3/Da / Density % sol: 64.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM ATP and Cysteine in 3.4M sodium malonate. The cysteinyl-AMP intermediate formed during the soak. ...Details: 1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM ATP and Cysteine in 3.4M sodium malonate. The cysteinyl-AMP intermediate formed during the soak. plate Liu-S-192 G6 Puck: PSL-0210, Cryo: direct from soaking solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 20, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.22→47.82 Å / Num. obs: 77956 / % possible obs: 100 % / Redundancy: 19.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.032 / Rrim(I) all: 0.144 / Χ2: 1.11 / Net I/σ(I): 20 / Num. measured all: 1546532
Reflection shellResolution: 2.22→2.28 Å / % possible obs: 100 % / Redundancy: 19.8 % / Rmerge(I) obs: 2.365 / Num. measured all: 111657 / Num. unique obs: 5633 / CC1/2: 0.714 / Rpim(I) all: 0.542 / Rrim(I) all: 2.427 / Χ2: 0.96 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(2.0_5847: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→47.82 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2048 3947 5.07 %
Rwork0.1757 --
obs0.1772 77823 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7093 0 161 255 7509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017468
X-RAY DIFFRACTIONf_angle_d0.96310091
X-RAY DIFFRACTIONf_dihedral_angle_d18.0612746
X-RAY DIFFRACTIONf_chiral_restr0.0541072
X-RAY DIFFRACTIONf_plane_restr0.0081261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.250.22641510.24832536X-RAY DIFFRACTION100
2.25-2.280.26791600.24432576X-RAY DIFFRACTION100
2.28-2.310.27911470.24652595X-RAY DIFFRACTION100
2.31-2.340.28031520.23132565X-RAY DIFFRACTION100
2.34-2.370.30671250.2362582X-RAY DIFFRACTION100
2.37-2.410.26811320.22722623X-RAY DIFFRACTION100
2.41-2.440.22951450.20692600X-RAY DIFFRACTION100
2.44-2.480.23291370.20272586X-RAY DIFFRACTION100
2.48-2.530.23191300.19782586X-RAY DIFFRACTION100
2.53-2.570.25851300.20462609X-RAY DIFFRACTION100
2.57-2.620.22731440.21292611X-RAY DIFFRACTION100
2.62-2.680.2591280.22652618X-RAY DIFFRACTION100
2.68-2.730.30541180.24772640X-RAY DIFFRACTION100
2.73-2.80.31131500.25022583X-RAY DIFFRACTION100
2.8-2.870.28151420.2282615X-RAY DIFFRACTION100
2.87-2.940.24731290.21112615X-RAY DIFFRACTION100
2.94-3.030.26541410.19622621X-RAY DIFFRACTION100
3.03-3.130.25661310.19432633X-RAY DIFFRACTION100
3.13-3.240.24091480.18912657X-RAY DIFFRACTION100
3.24-3.370.22031330.18212622X-RAY DIFFRACTION100
3.37-3.520.23451500.16832648X-RAY DIFFRACTION100
3.52-3.710.17121500.14032645X-RAY DIFFRACTION100
3.71-3.940.14241470.13142655X-RAY DIFFRACTION100
3.94-4.250.14181420.12332688X-RAY DIFFRACTION100
4.25-4.670.15541540.12262677X-RAY DIFFRACTION100
4.67-5.350.12951340.13262735X-RAY DIFFRACTION100
5.35-6.730.19061440.18512786X-RAY DIFFRACTION100
6.74-47.820.22631530.19852969X-RAY DIFFRACTION100
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)
11.2489-0.2936-0.6192.59790.23361.6412-0.00560.15550.166-0.0783-0.0625-0.1416-0.15440.06980.07760.3892-0.0267-0.07520.35250.06630.379230.3027-30.90570.1247
21.56171.60360.36385.01080.84622.77110.00140.29570.1317-0.5832-0.02-0.1896-0.4004-0.08190.0550.67280.0334-0.02910.49580.18140.460627.3403-15.7131-18.0438
30.9865-0.2906-0.24681.4083-0.31722.1658-0.04380.20810.1448-0.1745-0.01520.0179-0.1354-0.1880.03970.3913-0.0314-0.08590.33480.05160.348722.717-30.7238-0.6781
41.894-1.55940.55272.3017-0.95880.9372-0.2084-0.1501-0.30170.16460.17880.22540.1569-0.09270.02280.4055-0.0380.03620.34260.03620.376429.4598-57.521117.455
51.2064-0.0467-0.13351.2113-0.52682.8903-0.10110.012-0.115-0.04260.0341-0.02670.2550.10070.07020.33960.0360.06190.30180.03010.339251.0311-67.095715.5356
62.31210.4501-0.90122.6224-0.33952.9096-0.05920.1128-0.5488-0.07370.056-0.03950.54380.08380.02360.69890.10160.13780.32490.00690.63554.1063-90.406913.5716
71.23230.17660.21021.87960.25521.3136-0.13260.0468-0.06010.02170.0519-0.20340.16210.24140.06190.42010.04730.08150.40390.05070.405458.293-67.885715.0092
81.571-1.34140.70692.6628-0.67551.286-0.15080.0680.47180.0807-0.0103-0.4663-0.31820.14490.15860.4179-0.0913-0.02320.40450.07890.564151.979-35.99068.9838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 146 )
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 239 )
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 350 )
4X-RAY DIFFRACTION4chain 'A' and (resid 351 through 458 )
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 146 )
6X-RAY DIFFRACTION6chain 'B' and (resid 147 through 239 )
7X-RAY DIFFRACTION7chain 'B' and (resid 240 through 348 )
8X-RAY DIFFRACTION8chain 'B' and (resid 349 through 458 )

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