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- PDB-6pr9: S. aureus dihydrofolate reductase co-crystallized with 1-ethylpro... -

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Basic information

Entry
Database: PDB / ID: 6pr9
TitleS. aureus dihydrofolate reductase co-crystallized with 1-ethylpropyl-dihydropthalazine inhibitor and NADP(H)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/INHIBITOR / DIHYDROFOLATE REDUCTASE / OXIDOREDUCTASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
Similarity search - Function
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-OWV / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsBourne, C.R. / Thomas, L.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI090685-01 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Inhibitor design to target a unique feature in the folate pocket of Staphylococcus aureus dihydrofolate reductase.
Authors: Muddala, N.P. / White, J.C. / Nammalwar, B. / Pratt, I. / Thomas, L.M. / Bunce, R.A. / Berlin, K.D. / Bourne, C.R.
History
DepositionJul 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 2.0Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0565
Polymers18,6111
Non-polymers1,4444
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.980, 78.980, 107.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Dihydrofolate reductase / / DHFR


Mass: 18611.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A017, dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-OWV / (2E)-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1S)-1-(pentan-3-yl)-3,4-dihydrophthalazin-2(1H)-yl]prop-2-en-1-one


Mass: 516.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H36N6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 297 K / Method: vapor diffusion / Details: 20% PEG6000, 0.1M MES, 0.15M Na Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2011 / Details: Osmic Mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→23.3 Å / Num. obs: 13732 / % possible obs: 99.5 % / Redundancy: 11.3 % / Biso Wilson estimate: 22.02 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.9
Reflection shellResolution: 2.01→2.08 Å / Rmerge(I) obs: 0.284 / Num. unique obs: 1357

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
CrystalCleardata collection
PHASER1.15.2_3472phasing
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M08

3m08


Resolution: 2.01→23.291 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.86
RfactorNum. reflection% reflection
Rfree0.2187 689 5.02 %
Rwork0.1722 --
obs0.1747 13729 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.79 Å2 / Biso mean: 25.4 Å2 / Biso min: 9.19 Å2
Refinement stepCycle: final / Resolution: 2.01→23.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 98 164 1572
Biso mean--25.72 34.17 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071489
X-RAY DIFFRACTIONf_angle_d1.2462035
X-RAY DIFFRACTIONf_chiral_restr0.049221
X-RAY DIFFRACTIONf_plane_restr0.005250
X-RAY DIFFRACTIONf_dihedral_angle_d20.468566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.01-2.16310.25771260.19482536100
2.1631-2.38060.23521520.19592560100
2.3806-2.72460.26071240.19952595100
2.7246-3.4310.2471360.17142616100
3.431-23.2910.17471510.1489273398

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