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- PDB-9yt5: Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasm... -

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Basic information

Entry
Database: PDB / ID: 9yt5
TitleCrystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with GMP
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
GUANOSINE-5'-MONOPHOSPHATE / MALONATE ION / cysteine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 GMP
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionOct 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 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)111,00213
Polymers109,0662
Non-polymers1,93611
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-91 kcal/mol
Surface area33470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.039, 120.039, 365.178
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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 , 5 types, 17 molecules

#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.48 Å3/Da / Density % sol: 64.67 %
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. 7 day soak with 10 mM GMP in 3.4M sodium malonate. plate Liu-S-192 H7 Puck: PSL-2106, 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: Oct 4, 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: 2.9→50.15 Å / Num. obs: 35643 / % possible obs: 100 % / Redundancy: 19.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.043 / Rrim(I) all: 0.189 / Χ2: 1.31 / Net I/σ(I): 19.5 / Num. measured all: 684905
Reflection shellResolution: 2.9→2.98 Å / % possible obs: 100 % / Redundancy: 18.5 % / Rmerge(I) obs: 2.318 / Num. measured all: 47512 / Num. unique obs: 2570 / CC1/2: 0.652 / Rpim(I) all: 0.551 / Rrim(I) all: 2.384 / Χ2: 1 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(2.0_5765: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50.15 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2153 1802 5.07 %
Rwork0.1855 --
obs0.187 35539 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→50.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7075 0 121 6 7202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067396
X-RAY DIFFRACTIONf_angle_d0.61710019
X-RAY DIFFRACTIONf_dihedral_angle_d15.1222739
X-RAY DIFFRACTIONf_chiral_restr0.0421068
X-RAY DIFFRACTIONf_plane_restr0.0061251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.980.30491340.2872532X-RAY DIFFRACTION100
2.98-3.070.34021460.28112527X-RAY DIFFRACTION100
3.07-3.160.31771340.27052540X-RAY DIFFRACTION100
3.17-3.280.30051240.24782534X-RAY DIFFRACTION100
3.28-3.410.23081300.20862575X-RAY DIFFRACTION100
3.41-3.560.21911410.18452539X-RAY DIFFRACTION100
3.56-3.750.21741410.17132578X-RAY DIFFRACTION100
3.75-3.990.1891260.15922566X-RAY DIFFRACTION100
3.99-4.30.15331400.14522592X-RAY DIFFRACTION100
4.3-4.730.19211500.13682583X-RAY DIFFRACTION100
4.73-5.410.17351300.15272637X-RAY DIFFRACTION100
5.41-6.810.23571620.21092654X-RAY DIFFRACTION100
6.81-50.150.21241440.19982880X-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)
1-0.54170.43280.33320.78050.07630.55860.11050.31580.0557-0.5102-0.1884-0.1320.0188-0.079300.87220.0435-0.01570.53750.04830.631329.8401-38.8044-4.9877
20.03520.37660.32610.50550.30190.18150.02060.27530.30390.1825-0.125-0.36-0.2371-0.0006-0.13130.95910.03150.07210.44190.19120.653828.8373-22.04122.4559
30.378-0.2139-0.51850.90410.88070.59410.0776-0.04870.32320.1723-0.1558-0.2017-0.34650.1319-0.00270.7528-0.0133-0.00370.48110.1540.742233.4059-20.52761.673
40.5109-0.13040.52840.2510.07710.63020.02480.73370.2723-0.39710.1840.2402-0.2416-0.1094-01.17380.1080.12460.96610.26740.830324.7663-21.0207-22.4709
5-0.2297-0.3687-0.22880.0249-0.98730.73020.16220.28580.2021-0.2029-0.2934-0.06910.01550.0241-0.00830.98190.05420.04640.57190.21780.746927.5314-21.9574-11.0966
60.7345-0.03120.48410.40040.27530.4848-0.08960.02060.2038-0.0851-0.17770.0748-0.1761-0.294600.6647-0.0181-0.13090.51580.05940.596416.5299-31.839212.8228
71.4746-1.16950.06483.3222-0.34921.5582-0.1926-0.0821-0.27940.01240.20470.33990.148-0.097400.6645-0.03250.01140.4980.09560.575627.4346-55.274216.1888
80.2255-0.55640.08360.01810.26650.10470.23340.3126-0.3031-0.1108-0.17050.0651-0.0197-0.2868-00.90710.09290.13520.79930.07360.593848.9529-67.3209-1.7239
91.1601-0.0757-0.42010.5344-0.23080.70020.0629-0.12630.00670.03960.034-0.07940.05470.1679-00.73520.08040.03570.53560.07590.627250.7836-69.95422.4176
100.5616-0.4874-0.33281.2719-0.0174-0.2563-0.00520.3373-0.281-0.1324-0.0137-0.15770.01540.1789-0.00020.90650.09670.09030.56470.01790.749354.387-83.689211.7572
110.4404-0.3977-0.1523-0.04510.26620.61-0.166-0.75390.36330.19380.1323-0.3413-0.07660.250600.72840.03310.03430.73460.19190.853164.3824-57.39224.0503
121.1421-0.91480.58241.15720.11441.52560.05270.20090.2997-0.3445-0.1258-0.56580.00490.0799-00.6249-0.08370.1080.54790.17060.900753.6019-38.43069.4073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 113 )
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 159 )
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 193 )
5X-RAY DIFFRACTION5chain 'A' and (resid 194 through 302 )
6X-RAY DIFFRACTION6chain 'A' and (resid 303 through 335 )
7X-RAY DIFFRACTION7chain 'A' and (resid 336 through 458 )
8X-RAY DIFFRACTION8chain 'B' and (resid 12 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 159 )
10X-RAY DIFFRACTION10chain 'B' and (resid 160 through 302 )
11X-RAY DIFFRACTION11chain 'B' and (resid 303 through 334 )
12X-RAY DIFFRACTION12chain 'B' and (resid 335 through 458 )

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