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- PDB-2blb: X-ray crystal structure of Plasmodium vivax dihydrofolate reducta... -

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Basic information

Entry
Database: PDB / ID: 2blb
TitleX-ray crystal structure of Plasmodium vivax dihydrofolate reductase in complex with pyrimethamine and its derivative
ComponentsDIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE
KeywordsOXIDOREDUCTASE / DIHYDROFOLATE REDUCTASE / PLAMODIUM VIVAX / PYRIMETHAMINE / MALARIA / DRUG RESISTANCE
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / methylation
Similarity search - Function
Bifunctional dihydrofolate reductase/thymidylate synthase / 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 ...Bifunctional dihydrofolate reductase/thymidylate synthase / 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 / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-ETHYL-5-PHENYLPYRIMIDINE-2,4-DIAMINE / Chem-NDP / Bifunctional dihydrofolate reductase-thymidylate synthase / Bifunctional dihydrofolate reductase-thymidylate synthase
Similarity search - Component
Biological speciesPLASMODIUM VIVAX (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKongsaeree, P. / Khongsuk, P. / Leartsakulpanich, U. / Chitnumsub, P. / Tarnchompoo, B. / Walkinshaw, M.D. / Yuthavong, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Crystal Structure of Dihydrofolate Reductase from Plasmodium Vivax: Pyrimethamine Displacement Linked with Mutation-Induced Resistance.
Authors: Kongsaeree, P. / Khongsuk, P. / Leartsakulpanich, U. / Chitnumsub, P. / Tarnchompoo, B. / Walkinshaw, M.D. / Yuthavong, Y.
History
DepositionMar 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2664
Polymers27,1111
Non-polymers1,1553
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)130.480, 55.570, 45.270
Angle α, β, γ (deg.)90.00, 106.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE / DIHYDROFOLATE REDUCTASE


Mass: 27110.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM VIVAX (malaria parasite P. vivax)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9TW60, UniProt: O02604*PLUS, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-CP7 / 6-ETHYL-5-PHENYLPYRIMIDINE-2,4-DIAMINE


Mass: 214.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.94 Å3/Da / Density % sol: 57.81 %
Crystal growDetails: 30%PEG4000, 100MM MES, PH 6.0, 10% GLYCEROL

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: NONIUS / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→19.1 Å / Num. obs: 7000 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.1
Reflection shellResolution: 2.89→3 Å / Redundancy: 3.02 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / % possible all: 88.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→5 Å / Rfactor Rfree error: 0.016 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.3 347 5.5 %RANDOM
Rwork0.192 ---
obs0.192 6307 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.9701 Å2 / ksol: 0.338446 e/Å3
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1-20.76 Å20 Å21.59 Å2
2---4.85 Å20 Å2
3----15.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 3→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 76 65 1910
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_deg1.4
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_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.671.5
X-RAY DIFFRACTIONc_mcangle_it9.242
X-RAY DIFFRACTIONc_scbond_it9.72
X-RAY DIFFRACTIONc_scangle_it11.642.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 55 5.3 %
Rwork0.281 975 -
obs--99.9 %

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