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- PDB-9z4d: Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasm... -

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Basic information

Entry
Database: PDB / ID: 9z4d
TitleCrystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Hexagonal P form)
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
cysteine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 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 (Hexagonal form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionNov 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 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)109,38510
Polymers109,0662
Non-polymers3198
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.174, 120.174, 363.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#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
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 3.47 Å3/Da / Density % sol: 64.56 %
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. Crystals were obtained as the GSU complex and soaked for 2 weeks with 10 mM Histidine in cryoprotectant. This displaced ...Details: 1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. Crystals were obtained as the GSU complex and soaked for 2 weeks with 10 mM Histidine in cryoprotectant. This displaced the GSU ligand resulting in an apo structure. Histidine was not bound. plate Liu-S-192 H8 , Puck: PSL-0115, Cryo: 3.4M sodium malonate

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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: Nov 1, 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: 2.87→50.02 Å / Num. obs: 36614 / % possible obs: 100 % / Redundancy: 38.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.037 / Rrim(I) all: 0.233 / Χ2: 1.21 / Net I/σ(I): 20.4 / Num. measured all: 1420633
Reflection shellResolution: 2.87→2.94 Å / % possible obs: 100 % / Redundancy: 41.9 % / Rmerge(I) obs: 3.959 / Num. measured all: 110623 / Num. unique obs: 2643 / CC1/2: 0.638 / Rpim(I) all: 0.611 / Rrim(I) all: 4.006 / Χ2: 1.04 / Net I/σ(I) obs: 1.6

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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: 2.87→47.81 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 1738 4.76 %
Rwork0.2154 --
obs0.2164 36503 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.87→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7045 0 8 2 7055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057246
X-RAY DIFFRACTIONf_angle_d0.5639803
X-RAY DIFFRACTIONf_dihedral_angle_d12.4462609
X-RAY DIFFRACTIONf_chiral_restr0.0421050
X-RAY DIFFRACTIONf_plane_restr0.0041236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-2.950.36921490.35852796X-RAY DIFFRACTION100
2.95-3.050.33861410.30752833X-RAY DIFFRACTION100
3.05-3.160.31231350.28692874X-RAY DIFFRACTION100
3.16-3.290.30511530.27992798X-RAY DIFFRACTION100
3.29-3.430.31841400.29162864X-RAY DIFFRACTION100
3.43-3.620.27791230.24252864X-RAY DIFFRACTION100
3.62-3.840.21851180.20932894X-RAY DIFFRACTION100
3.84-4.140.23021470.20222886X-RAY DIFFRACTION100
4.14-4.550.19931470.17652897X-RAY DIFFRACTION100
4.55-5.210.20221680.17172915X-RAY DIFFRACTION100
5.21-6.560.25191410.21232982X-RAY DIFFRACTION100
6.57-47.810.2071760.20043162X-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)
10.0671-0.16650.05561.9067-0.09920.58190.10170.08320.1496-0.3827-0.2347-0.21780.11410.0012-0.00130.85330.0273-0.01130.49840.07480.689530.2947-30.89220.1573
20.5285-0.21830.06121.2286-0.80670.8910.06280.37840.0985-0.4016-0.1895-0.08660.135-0.1478-01.12820.0720.08930.65650.19120.691927.8734-21.381-14.2203
30.4752-0.11330.43380.20560.09220.597-0.29440.00270.29480.09740.00380.2053-0.2713-0.117600.8006-0.0024-0.12390.62920.05330.667116.3657-32.07312.7391
40.9326-1.10630.05482.5483-0.44370.6717-0.1498-0.1183-0.2566-0.24140.16580.34220.1654-0.23600.8094-0.0377-0.00780.57270.06580.642227.4306-55.434316.0175
51.463-0.5525-0.28461.1075-0.2640.37590.07540.086-0.0024-0.2823-0.082-0.20810.20680.032400.8830.12290.12920.53690.09440.692650.5505-71.673215.3284
61.6709-1.19970.26591.2697-0.20370.0250.12930.2119-0.1083-0.1168-0.0431-0.0688-0.01960.0467-01.08770.09720.15020.63050.00630.768354.6456-84.666413.2189
71.7691-0.6067-0.01230.7104-0.24440.62970.00410.13520.1268-0.13-0.1103-0.67460.26060.0404-00.9540.07990.13720.64830.14980.889160.8074-64.748715.4073
80.09560.13090.14330.19350.20120.2094-0.0491-0.45260.0936-0.4270.4182-0.2815-0.2198-0.368300.7387-0.03660.00710.65010.10561.19756.7776-37.109918.3514
9-0.0102-0.01110.00090.657-0.77130.8830.04920.3190.5536-0.2423-0.2868-1.02250.0940.129-00.90870.02220.15880.65360.27291.208751.7807-35.72273.8372
100.49380.1591-0.21680.06720.01390.4784-0.2003-0.29650.4528-0.0032-0.1158-0.63830.2143-0.3504-0.01970.84380.02690.10350.58910.17731.083447.8621-37.426510.7081
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 302 )
3X-RAY DIFFRACTION3chain 'A' and (resid 303 through 335 )
4X-RAY DIFFRACTION4chain 'A' and (resid 336 through 458 )
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 174 )
6X-RAY DIFFRACTION6chain 'B' and (resid 175 through 272 )
7X-RAY DIFFRACTION7chain 'B' and (resid 273 through 348 )
8X-RAY DIFFRACTION8chain 'B' and (resid 349 through 374 )
9X-RAY DIFFRACTION9chain 'B' and (resid 375 through 431 )
10X-RAY DIFFRACTION10chain 'B' and (resid 432 through 458 )

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