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- PDB-3qgt: Crystal structure of Wild-type PfDHFR-TS COMPLEXED WITH NADPH, dU... -

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Basic information

Entry
Database: PDB / ID: 3qgt
TitleCrystal structure of Wild-type PfDHFR-TS COMPLEXED WITH NADPH, dUMP AND PYRIMETHAMINE
ComponentsBifunctional dihydrofolate reductase-thymidylate synthase
KeywordsOXIDOREDUCTASE / TRANSFERASE/INHIBITOR / malarial DHFR-TS antifolate complex / rossmann fold / reductase / Dihydrofolate binding / dUMP binding / NADPH binding / TRANSFERASE-INHIBITOR complex
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
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, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / 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, 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 / 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-CP6 / Chem-NDP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Bifunctional dihydrofolate reductase-thymidylate synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsChitnumsub, P. / Yuthavong, Y.
CitationJournal: Acs Chem.Biol. / Year: 2011
Title: Trypanosomal dihydrofolate reductase reveals natural antifolate resistance
Authors: Vanichtanankul, J. / Taweechai, S. / Yuvaniyama, J. / Vilaivan, T. / Chitnumsub, P. / Kamchonwongpaisan, S. / Yuthavong, Y.
History
DepositionJan 24, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Nov 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,2618
Polymers143,6562
Non-polymers2,6056
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-33 kcal/mol
Surface area49030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.096, 154.436, 164.005
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 Bifunctional dihydrofolate reductase-thymidylate synthase


Mass: 71828.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: TM4 / Gene: DHFR-TS / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A7UD81, dihydrofolate reductase, thymidylate synthase
#2: Chemical ChemComp-CP6 / 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE / PYRIMETHAMINE


Mass: 248.711 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13ClN4 / Comment: medication, antiparasitic*YM
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-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


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


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ENTIRE PROTEIN (INCLUDING 2 DOMAINS: REDUCTASE DOMAIN: RESIDUES 1-231; SYNTHASE DOMAIN: ...THE ENTIRE PROTEIN (INCLUDING 2 DOMAINS: REDUCTASE DOMAIN: RESIDUES 1-231; SYNTHASE DOMAIN: RESIDUES 283-608) WAS EXPRESSED IN ONE POLYPEPTIDE CHAIN. SINCE THE DENSITY OF THE JUNCTION PEPTIDES (RESIDUES 232-282) BETWEEN THE TWO DOMAINS ARE NOT VISIBLE FOR BOTH MONOMERS, THERE IS STILL AMBIGUITY REGARDING HOW THE TWO DOMAINS ARE PHYSIOLOGICALLY CONNECTED, HENCE A(1-231)-A(283-608) AND B(1-231)-B(283-608), OR ANOTHER CASE, A(1-231)-B(283-608) AND B(1-231)-A(283-608).

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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: 2.47 Å3/Da / Density % sol: 50.25 % / Mosaicity: 0.604 °
Crystal growTemperature: 297 K / Method: microbatch / pH: 4.5
Details: PEG 4000, NH4OAc, pH 4.5, microbatch, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Aug 29, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 16.03 / Number: 294701 / Rmerge(I) obs: 0.082 / Χ2: 1.55 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 63667 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.955099.810.0561.208
3.934.9599.910.0551.501
3.443.9310010.0751.747
3.123.4499.810.1091.818
2.93.1210010.1581.736
2.732.999.910.2191.686
2.592.7399.810.2811.653
2.482.5999.210.3491.627
2.382.4898.610.4131.478
2.32.389610.4681.449
ReflectionResolution: 2.3→50 Å / Num. obs: 63667 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 33.9 / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.55 / Net I/σ(I): 16.027
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.380.4682.3460341.449196
2.38-2.480.4132.9562581.478198.6
2.48-2.590.3493.9262471.627199.2
2.59-2.730.2815.4263471.653199.8
2.73-2.90.2197.463391.686199.9
2.9-3.120.15810.9163871.7361100
3.12-3.440.10917.7963441.818199.8
3.44-3.930.07525.4764321.7471100
3.93-4.950.05532.3465101.501199.9
4.95-500.05634.3867691.208199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
superguidata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J3I

1j3i


Resolution: 2.3→44.62 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8204 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2596 3186 5 %RANDOM
Rwork0.2217 ---
all-64107 --
obs-63588 98.9 %-
Solvent computationBsol: 48.7924 Å2
Displacement parametersBiso max: 121.8 Å2 / Biso mean: 43.0398 Å2 / Biso min: 13.08 Å2
Baniso -1Baniso -2Baniso -3
1-4.961 Å20 Å20 Å2
2---0.722 Å20 Å2
3----4.239 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9044 0 170 313 9527
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0071.5
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scangle_it2.742.5
X-RAY DIFFRACTIONc_torsion_deg23
X-RAY DIFFRACTIONc_torsion_impr_deg0.77
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.410.3064050.2868300.015866752795.3
2.41-2.530.3253480.27711740.0171250782798.6
2.53-2.690.2954160.25911770.0141249788399.5
2.69-2.90.2783880.23811300.0141188793499.8
2.9-3.190.2794110.21911930.0141258794799.8
3.19-3.650.2423800.19911720.0121236800799.8
3.65-4.60.214240.18511940.011262808099.9
4.6-44.620.254140.21212110.0121262838399.8
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2ligands_1.param
X-RAY DIFFRACTION3CNS_TOPPAR:water.param

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