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- PDB-6prb: S. aureus dihydrofolate reductase co-crystallized with cyclopropy... -

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Basic information

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


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol
Similarity search - Function
Dihydrofolate reductase / 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 / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-OWM / Chem-R0Y / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5365
Polymers18,6111
Non-polymers1,9254
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.090, 79.090, 105.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 132 molecules

#2: Chemical ChemComp-R0Y / (2E)-1-[(1S)-1-cyclopropyl-6,7-dimethoxy-3,4-dihydrophthalazin-2(1H)-yl]-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}prop-2-en-1-one


Mass: 544.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32N6O5
#3: Chemical ChemComp-OWM / (2E)-1-[(1R)-1-cyclopropyl-6,7-dimethoxyphthalazin-2(1H)-yl]-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}prop-2-en-1-one


Mass: 544.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32N6O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 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 MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 20, 2015
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→41.9 Å / Num. obs: 13803 / % possible obs: 96.9 % / Redundancy: 14.4 % / Biso Wilson estimate: 27.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Net I/σ(I): 37.2
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.482 / Num. unique obs: 675 / CC1/2: 0.973

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M08

3m08


Resolution: 2→41.83 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 1336 10 %
Rwork0.1873 --
obs0.1924 13354 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→41.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 134 128 1576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141477
X-RAY DIFFRACTIONf_angle_d1.7632021
X-RAY DIFFRACTIONf_dihedral_angle_d25.076591
X-RAY DIFFRACTIONf_chiral_restr0.235222
X-RAY DIFFRACTIONf_plane_restr0.005247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.07160.31371320.21241197X-RAY DIFFRACTION99
2.0716-2.15460.24161330.17941197X-RAY DIFFRACTION100
2.1546-2.25260.25211350.19041222X-RAY DIFFRACTION100
2.2526-2.37140.27821350.20511200X-RAY DIFFRACTION99
2.3714-2.51990.34961290.20821184X-RAY DIFFRACTION97
2.5199-2.71450.30781210.22971125X-RAY DIFFRACTION91
2.7145-2.98760.2731270.22011077X-RAY DIFFRACTION88
2.9876-3.41970.2241310.18911205X-RAY DIFFRACTION96
3.4197-4.30780.17031400.14441264X-RAY DIFFRACTION100
4.3078-41.83940.22831530.191347X-RAY DIFFRACTION98

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