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- PDB-4fgh: S. aureus dihydrofolate reductase co-crystallized with ethyl-DAP ... -

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Basic information

Entry
Database: PDB / ID: 4fgh
TitleS. aureus dihydrofolate reductase co-crystallized with ethyl-DAP isobutenyl-dihydrophthalazine inhibitor
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/INHIBITOR / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


dihydrofolate metabolic process / glycine biosynthetic 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, 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
Chem-0U6 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / PDB entry 3M08 / Resolution: 2.5 Å
AuthorsBourne, C.R. / Barrow, W.W.
CitationJournal: Chemmedchem / Year: 2012
Title: Inhibition of Bacterial Dihydrofolate Reductase by 6-Alkyl-2,4-diaminopyrimidines.
Authors: Nammalwar, B. / Bourne, C.R. / Bunce, R.A. / Wakeham, N. / Bourne, P.C. / Ramnarayan, K. / Mylvaganam, S. / Berlin, K.D. / Barrow, E.W. / Barrow, W.W.
History
DepositionJun 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Apr 17, 2013Group: Database references
Revision 1.3Nov 20, 2013Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1054
Polymers18,7431
Non-polymers1,3623
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.921, 78.921, 106.178
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Dihydrofolate reductase / DHFR


Mass: 18742.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: DHFR, folA / Plasmid: pET-101D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0A017, dihydrofolate reductase
#2: 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
#3: Chemical ChemComp-0U6 / (2E)-3-{5-[(2,4-diamino-6-ethylpyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1S)-1-(2-methylprop-1-en-1-yl)phthalazin-2(1H)-yl]prop-2-en-1-one


Mass: 526.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H34N6O3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15-20% PEG 6000, 0.15M NaOAc, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→70 Å / Num. obs: 7223 / % possible obs: 100 % / Redundancy: 36 % / Rsym value: 0.16 / Net I/σ(I): 19.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.2_869) / Classification: refinement
RefinementMethod to determine structure: PDB entry 3M08 / Resolution: 2.5→68.348 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 723 10.02 %
Rwork0.1916 --
obs0.1972 7218 99.94 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.874 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.9774 Å20 Å20 Å2
2---4.9774 Å2-0 Å2
3---9.9548 Å2
Refinement stepCycle: LAST / Resolution: 2.5→68.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 93 69 1478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081449
X-RAY DIFFRACTIONf_angle_d1.1841975
X-RAY DIFFRACTIONf_dihedral_angle_d23.655577
X-RAY DIFFRACTIONf_chiral_restr0.087219
X-RAY DIFFRACTIONf_plane_restr0.006239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.69320.30371400.22421257X-RAY DIFFRACTION100
2.6932-2.96430.26291360.21711265X-RAY DIFFRACTION100
2.9643-3.39320.27641470.19741275X-RAY DIFFRACTION100
3.3932-4.2750.23181460.17671299X-RAY DIFFRACTION100
4.275-68.37310.21231540.17761399X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -2.0358 Å / Origin y: 26.5153 Å / Origin z: -1.9318 Å
111213212223313233
T0.1852 Å20.0277 Å20.0374 Å2-0.0731 Å2-0.0136 Å2--0.1604 Å2
L2.3701 °20.8309 °2-0.3747 °2-2.1357 °20.1026 °2--2.3924 °2
S0.0303 Å °-0.144 Å °0.2099 Å °0.1396 Å °0.0371 Å °-0.091 Å °-0.2995 Å °-0.0029 Å °-0.0585 Å °
Refinement TLS groupSelection details: chain 'A' and (resseq 0:162)

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