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- PDB-3dga: Wild-type Plasmodium falciparum dihydrofolate reductase-thymidyla... -

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Basic information

Entry
Database: PDB / ID: 3dga
TitleWild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with RJF01302, NADPH, and dUMP
Components(Bifunctional dihydrofolate reductase-thymidylate ...) x 2
KeywordsOXIDOREDUCTASE / TRANSFERASE / Alpha-Beta / Methyltransferase
Function / homology
Function and homology information


Interconversion of nucleotide di- and triphosphates / thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / mitochondrion ...Interconversion of nucleotide di- and triphosphates / thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / mitochondrion / RNA binding / cytoplasm / cytosol
Similarity search - Function
Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / 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/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / 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 domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Chem-RJ1 / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Bifunctional dihydrofolate reductase-thymidylate synthase / Bifunctional dihydrofolate reductase-thymidylate synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsDasgupta, T. / Chitnumsub, P. / Maneeruttanarungroj, C. / Kamchonwongpaisan, S. / Nichols, S. / Lyons, T.M. / Tirado-Rives, J. / Jorgensen, W.L. / Yuthavong, Y. / Anderson, K.S.
CitationJournal: Acs Chem.Biol. / Year: 2009
Title: Exploiting structural analysis, in silico screening, and serendipity to identify novel inhibitors of drug-resistant falciparum malaria.
Authors: Dasgupta, T. / Chitnumsub, P. / Kamchonwongpaisan, S. / Maneeruttanarungroj, C. / Nichols, S.E. / Lyons, T.M. / Tirado-Rives, J. / Jorgensen, W.L. / Yuthavong, Y. / Anderson, K.S.
History
DepositionJun 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)146,35910
Polymers143,6924
Non-polymers2,6676
Water4,486249
1
A: Bifunctional dihydrofolate reductase-thymidylate synthase
C: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1795
Polymers71,8462
Non-polymers1,3333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-7.1 kcal/mol
Surface area28110 Å2
MethodPISA
2
B: Bifunctional dihydrofolate reductase-thymidylate synthase
D: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1795
Polymers71,8462
Non-polymers1,3333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-7.9 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.377, 156.015, 164.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is the same as asymmetric unit.

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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: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8I1R6, UniProt: P13922*PLUS, 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: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8I1R6, UniProt: P13922*PLUS, dihydrofolate reductase, thymidylate synthase

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Non-polymers , 4 types, 255 molecules

#3: Chemical ChemComp-RJ1 / N-[2-chloro-5-(trifluoromethyl)phenyl]imidodicarbonimidic diamide / 2-{[{[amino(imino)methyl]amino}(imino)methyl]amino}-1-chloro-4-(trifluoromethyl)benzene


Mass: 279.649 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9ClF3N5
#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.: 249 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE INFORMATION PROVIDED BY AUTHORS IS THE GENBANK ENTRY ABU43156.1

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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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 297 K / pH: 4.6
Details: PEG 4000, NH4OAc, pH 4.6, MICROBATCH, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54178
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Nov 6, 2007 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 41385 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 18.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.17 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 4.41 / Rsym value: 0.299 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1J3I

1j3i


Resolution: 2.7→29.18 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2081 5 %RANDOM
Rwork0.205 ---
obs0.205 41385 99.7 %-
all-41385 --
Solvent computationBsol: 28.65 Å2
Displacement parametersBiso mean: 44.15 Å2
Baniso -1Baniso -2Baniso -3
1--17.649 Å20 Å20 Å2
2--3.115 Å20 Å2
3---14.534 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-4 Å
Luzzati sigma a0.52 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9094 0 172 249 9515
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.225
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_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4061.5
X-RAY DIFFRACTIONc_mcangle_it2.4562
X-RAY DIFFRACTIONc_scbond_it1.7712
X-RAY DIFFRACTIONc_scangle_it2.72.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2LIGANDS_1.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:WATER_REP.PARAM

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