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

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Basic information

Entry
Database: PDB / ID: 9yrz
TitleCrystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with 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 MONOPHOSPHATE / MALONATE ION / cysteine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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 AMP
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionOct 17, 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)111,18817
Polymers109,0662
Non-polymers2,12215
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-100 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.002, 120.002, 366.400
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-727-

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 , 5 types, 353 molecules

#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 5 / 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.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 64.77 %
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 AMP in 3.4M sodium malonate. Liu-S-192 E1, Puck: PSL-0203, 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: 2.06→47.81 Å / Num. obs: 97237 / % possible obs: 100 % / Redundancy: 39.5 % / CC1/2: 1 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.023 / Rrim(I) all: 0.144 / Χ2: 1.11 / Net I/σ(I): 26.1 / Num. measured all: 3845221
Reflection shellResolution: 2.06→2.11 Å / % possible obs: 100 % / Redundancy: 40.1 % / Rmerge(I) obs: 3.233 / Num. measured all: 282028 / Num. unique obs: 7030 / CC1/2: 0.736 / Rpim(I) all: 0.514 / Rrim(I) all: 3.274 / Χ2: 0.96 / 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: 2.06→47.81 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 4837 4.98 %
Rwork0.176 --
obs0.177 97084 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7081 0 133 338 7552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097427
X-RAY DIFFRACTIONf_angle_d0.92410056
X-RAY DIFFRACTIONf_dihedral_angle_d13.3072690
X-RAY DIFFRACTIONf_chiral_restr0.0521069
X-RAY DIFFRACTIONf_plane_restr0.0071258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.080.34411470.34263028X-RAY DIFFRACTION100
2.08-2.110.33241780.30873005X-RAY DIFFRACTION100
2.11-2.130.31561850.26182971X-RAY DIFFRACTION100
2.13-2.160.27341520.24063023X-RAY DIFFRACTION100
2.16-2.190.2761510.22893060X-RAY DIFFRACTION100
2.19-2.220.27741470.21193007X-RAY DIFFRACTION100
2.22-2.250.21531450.19023028X-RAY DIFFRACTION100
2.25-2.280.19631390.1813045X-RAY DIFFRACTION100
2.28-2.320.19541600.17273045X-RAY DIFFRACTION100
2.32-2.360.2271450.17863034X-RAY DIFFRACTION100
2.36-2.40.20781890.17993017X-RAY DIFFRACTION100
2.4-2.440.21941810.18223013X-RAY DIFFRACTION100
2.44-2.490.21431550.18613035X-RAY DIFFRACTION100
2.49-2.540.21781510.19383053X-RAY DIFFRACTION100
2.54-2.60.23341590.20393038X-RAY DIFFRACTION100
2.6-2.660.25391550.22793054X-RAY DIFFRACTION100
2.66-2.720.25581680.23563054X-RAY DIFFRACTION100
2.72-2.80.27011800.21013026X-RAY DIFFRACTION100
2.8-2.880.22351540.20453066X-RAY DIFFRACTION100
2.88-2.970.24271690.20483067X-RAY DIFFRACTION100
2.97-3.080.23551760.19763055X-RAY DIFFRACTION100
3.08-3.20.20091590.19633064X-RAY DIFFRACTION100
3.2-3.350.20331660.18453106X-RAY DIFFRACTION100
3.35-3.520.18721600.15553094X-RAY DIFFRACTION100
3.52-3.740.1591540.14183124X-RAY DIFFRACTION100
3.74-4.030.15321390.12993134X-RAY DIFFRACTION100
4.03-4.440.12971640.1173160X-RAY DIFFRACTION100
4.44-5.080.14351700.12853155X-RAY DIFFRACTION100
5.08-6.40.18361700.17373229X-RAY DIFFRACTION100
6.4-47.810.18441690.20793457X-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)
10.6704-0.0653-0.33381.0142-0.14930.6760.00890.13180.1362-0.1375-0.0269-0.0985-0.08450.027900.4117-0.0231-0.04910.30460.06580.372930.9737-29.4381-1.2118
20.35960.1576-0.03010.5409-0.34660.76690.00210.26880.0994-0.2274-0.0189-0.0824-0.0675-0.0843-0.00430.4926-0.0131-0.00430.37140.13430.361826.9954-21.739-14.2557
30.20390.07520.16150.09780.15350.2085-0.1553-0.03130.0590.0790.04880.2222-0.0509-0.214600.42330.0056-0.06350.35630.01980.35416.6753-31.449413.0273
40.8777-0.7414-0.04631.1238-0.15720.2543-0.1583-0.0966-0.15390.08180.14480.210.0558-0.131300.4035-0.01240.01030.32990.04170.375127.4468-55.158216.2424
50.7141-0.0351-0.24660.6370.03690.7004-0.06280.028-0.0816-0.05220.02860.0010.13560.105600.37540.02890.04990.30470.03120.345751.0421-67.100715.6152
60.9663-0.33190.25140.79950.19610.1831-0.06590.0658-0.3344-0.00370.10520.0170.20870.0651-0.0030.58380.05070.12460.26650.01390.501153.1089-88.588914.1994
70.7952-0.63350.03120.6801-0.38570.5984-0.10960.01660.22530.0456-0.0195-0.2951-0.03850.151800.3658-0.03790.00230.34540.03730.425855.5525-49.378311.4504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 159 )
2X-RAY DIFFRACTION2chain 'A' and (resid 160 through 302 )
3X-RAY DIFFRACTION3chain 'A' and (resid 303 through 334 )
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 458 )
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 146 )
6X-RAY DIFFRACTION6chain 'B' and (resid 147 through 256 )
7X-RAY DIFFRACTION7chain 'B' and (resid 257 through 458 )

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