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- PDB-3jsu: Quadruple mutant(N51I+C59R+S108N+I164L) plasmodium falciparum dih... -

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Basic information

Entry
Database: PDB / ID: 3jsu
TitleQuadruple mutant(N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase(PFDHFR-TS) complexed with QN254, NADPH, and dUMP
ComponentsDihydrofolate reductase-thymidylate synthase
KeywordsOXIDOREDUCTASE / TRANSFERASE / Rossmann fold
Function / homology
Function and homology information


thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / nucleotide binding / mitochondrion / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2210 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2210 / 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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Dihydrofolate reductase-like domain superfamily / Helix non-globular / Special / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-KA5 / Chem-NDP / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChitnumsub, P. / Maneeruttanarungroj, C. / Kamchonwongpaisan, S. / Yuthavong, Y. / Diagana, T.T.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2010
Title: Preclinical evaluation of the antifolate QN254, 5-chloro- N'6'-(2,5-dimethoxy-benzyl)-quinazoline-2,4,6-triamine, as an antimalarial drug candidate
Authors: Nzila, A. / Rottmann, M. / Chitnumsub, P. / Kiara, S.M. / Kamchonwongpaisan, S. / Maneeruttanarungroj, C. / Taweechai, S. / Yeung, B.K. / Goh, A. / Lakshminarayana, S.B. / Zou, B. / Wong, J. ...Authors: Nzila, A. / Rottmann, M. / Chitnumsub, P. / Kiara, S.M. / Kamchonwongpaisan, S. / Maneeruttanarungroj, C. / Taweechai, S. / Yeung, B.K. / Goh, A. / Lakshminarayana, S.B. / Zou, B. / Wong, J. / Ma, N.L. / Weaver, M. / Keller, T.H. / Dartois, V. / Wittlin, S. / Brun, R. / Yuthavong, Y. / Diagana, T.T.
History
DepositionSep 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 1.3Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Dihydrofolate reductase-thymidylate synthase
B: Dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,6438
Polymers143,8162
Non-polymers2,8276
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-28 kcal/mol
Surface area49080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.991, 157.375, 165.511
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dihydrofolate reductase-thymidylate synthase / Bifunctional dihydrofolate reductase-thymidylate synthase


Mass: 71908.133 Da / Num. of mol.: 2 / Mutation: N51I,C59R,S108N,I164L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: V1/S / Gene: DHFR-TS, V1/S / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A7UD79, UniProt: D9N170*PLUS, dihydrofolate reductase, thymidylate synthase
#2: Chemical ChemComp-KA5 / 5-chloro-N~6~-(2,5-dimethoxybenzyl)quinazoline-2,4,6-triamine


Mass: 359.810 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18ClN5O2
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


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


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


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.67 Å3/Da / Density % sol: 53.95 % / Mosaicity: 0.49 °
Crystal growTemperature: 297 K / Method: vapor diffusion, microbatch / pH: 4.5
Details: PEG4000, NH4OAc, pH 4.5, vapor diffusion, microbatch, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Jan 31, 2008 / Details: mirror
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→45.39 Å / Num. all: 43195 / Num. obs: 43269 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 60.8 Å2 / Limit h max: 21 / Limit h min: 0 / Limit k max: 58 / Limit k min: 0 / Limit l max: 61 / Limit l min: 0 / Observed criterion F max: 2021629.36 / Observed criterion F min: 12.1 / Rsym value: 0.067 / Χ2: 1.273 / Net I/σ(I): 16
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.418 / Num. unique all: 4215 / Χ2: 1.469 / % possible all: 98.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.005data extraction
superguidata collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J3K

1j3k


Resolution: 2.7→29.5 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2163 5 %RANDOM
Rwork0.206 ---
all-43235 --
obs-43103 99.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 35.9363 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 90.56 Å2 / Biso mean: 49.47 Å2 / Biso min: 16.83 Å2
Baniso -1Baniso -2Baniso -3
1-11.79 Å20 Å20 Å2
2---6.61 Å20 Å2
3----5.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.39 Å
Luzzati d res high-2.7
Refinement stepCycle: LAST / Resolution: 2.7→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9050 0 186 251 9487
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.7-2.820.3432755.20.30949820.0215335525798.5
2.82-2.970.32795.30.27150140.0185318529399.5
2.97-3.160.292344.40.24350590.0195326529399.4
3.16-3.40.2682514.70.22650820.0175345533399.8
3.4-3.740.2432735.10.2151210.0155404539499.8
3.74-4.280.1982855.30.17151030.0125391538899.9
4.28-5.390.1882604.80.16252090.01254705469100
5.39-29.50.2143065.40.253700.01256775676100

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