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- PDB-1j3i: Wild-type Plasmodium falciparum dihydrofolate reductase-thymidyla... -

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Basic information

Entry
Database: PDB / ID: 1j3i
TitleWild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with WR99210, NADPH, and dUMP
Components(Bifunctional dihydrofolate reductase-thymidylate ...) x 2
KeywordsOXIDOREDUCTASE / TRANSFERASE / bifunctional
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / mitochondrion / cytosol
Similarity search - Function
Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase ...Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Chem-WRA / Bifunctional dihydrofolate reductase-thymidylate synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsYuvaniyama, J. / Chitnumsub, P. / Kamchonwongpaisan, S. / Vanichtanankul, J. / Sirawaraporn, W. / Taylor, P. / Walkinshaw, M. / Yuthavong, Y.
CitationJournal: NAT.STRUCT.BIOL. / Year: 2003
Title: Insights into antifolate resistance from malarial DHFR-TS structures.
Authors: Yuvaniyama, J. / Chitnumsub, P. / Kamchonwongpaisan, S. / Vanichtanankul, J. / Sirawaraporn, W. / Taylor, P. / Walkinshaw, M.D. / Yuthavong, Y.
History
DepositionFeb 3, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Bifunctional dihydrofolate reductase-thymidylate synthase
B: Bifunctional dihydrofolate reductase-thymidylate synthase
C: Bifunctional dihydrofolate reductase-thymidylate synthase
D: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,58910
Polymers143,6924
Non-polymers2,8976
Water14,196788
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17570 Å2
ΔGint-94 kcal/mol
Surface area48550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.117, 157.249, 165.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Bifunctional dihydrofolate reductase-thymidylate ... , 2 types, 4 molecules ABCD

#1: Protein Bifunctional dihydrofolate reductase-thymidylate synthase


Mass: 33133.180 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pLysS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P13922, dihydrofolate reductase, thymidylate synthase
#2: Protein Bifunctional dihydrofolate reductase-thymidylate synthase


Mass: 38712.949 Da / Num. of mol.: 2 / Fragment: RESIDUES 281-608
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pLysS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P13922, dihydrofolate reductase, thymidylate synthase

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Non-polymers , 4 types, 794 molecules

#3: Chemical ChemComp-WRA / 6,6-DIMETHYL-1-[3-(2,4,5-TRICHLOROPHENOXY)PROPOXY]-1,6-DIHYDRO-1,3,5-TRIAZINE-2,4-DIAMINE / 4,6-DIAMINO-1,2-DIHYDRO-2,2-DIMETHYL-1-[(2,4,5-TRICHLOROPHENOXY)PROPYLOXY]-1,3,5-TRIAZINE


Mass: 394.684 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18Cl3N5O2
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 788 / 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: 2.71 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 4.6
Details: PEG 4000, ammonium acetate, sodium acetate, pH 4.6, microbatch under oil, temperature 298K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlenzyme11
20.1 mMsodium acetate11pH4.6
325 %(w/v)PEG400011
40.2 Mammonium acetate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.33→33 Å / Num. obs: 64441 / % possible obs: 97.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 36.2 Å2 / Rsym value: 0.057 / Net I/σ(I): 10.4
Reflection shellResolution: 2.33→2.43 Å / Rsym value: 0.313 / % possible all: 89
Reflection
*PLUS
Lowest resolution: 33 Å / Num. measured all: 653647 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 89 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→29.4 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3211 5 %RANDOM
Rwork0.185 ---
all0.187 66849 --
obs0.187 64375 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.9581 Å2 / ksol: 0.322084 e/Å3
Displacement parametersBiso mean: 49.1 Å2
Baniso -1Baniso -2Baniso -3
1-12.25 Å20 Å20 Å2
2---5.16 Å20 Å2
3----7.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.33→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9163 0 184 788 10135
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.54
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 2.33→2.41 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.297 242 5.1 %
Rwork0.239 4547 -
obs--72.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2LIGANDS.PARAMLIGANDS.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 29.4 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.54

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