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- PDB-3f0s: Staphylococcus aureus dihydrofolate reductase complexed with NADP... -

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Basic information

Entry
Database: PDB / ID: 3f0s
TitleStaphylococcus aureus dihydrofolate reductase complexed with NADPH and 2,4-Diamino-5-[3-(3-methoxy-5-(3,5-dimethylphenyl)phenyl)but-1-ynyl]-6-methylpyrimidine
ComponentsTrimethoprim-sensitive dihydrofolate reductase
KeywordsOXIDOREDUCTASE
Function / homologyDihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / Chem-53T / Chem-NDP / :
Function and homology information
Biological speciesStaphylococcus aureus RF122 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsAnderson, A.C. / Frey, K.M. / Liu, J. / Lombardo, M.N.
CitationJournal: To be Published
Title: Crystallographic Complexes of Wildtype and Mutant MRSA DHFR Reveal Interactions for Lead Design
Authors: Frey, K.M. / Liu, J. / Lombardo, M.N. / Bolstad, D.B. / Smith, A.E. / Priestley, N.D. / Wright, D.L. / Anderson, A.C.
History
DepositionOct 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2013Group: Non-polymer description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Trimethoprim-sensitive dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1473
Polymers18,0161
Non-polymers1,1322
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.958, 78.958, 107.422
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 Trimethoprim-sensitive dihydrofolate reductase


Mass: 18015.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus RF122 (bacteria) / Gene: dfrB / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YY41, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-53T / 5-[(3R)-3-(5-methoxy-3',5'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine


Mass: 386.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26N4O

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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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15 % PEG 10000, 150 mM Sodium acetate, 100 mM MES pH 6.5, 5 % Butyrlactone, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.7→37.06 Å / Num. all: 5169 / Num. obs: 5169 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Χ2: 0.519 / Net I/σ(I): 3.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 4.7 / Num. unique all: 346 / Rsym value: 0.261 / Χ2: 0.39 / % possible all: 87.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Sa F98Y DHFR bound to Folate and NADPH (Dale et al., J.Mol.Biol. 1997, structure not deposited in the PDB)

Resolution: 2.7→37.06 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.857 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.107 / SU ML: 0.271 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 245 4.5 %RANDOM
Rwork0.201 ---
all0.204 5169 --
obs0.204 5169 92.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.53 Å2 / Biso mean: 21.087 Å2 / Biso min: 3.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.7→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 77 0 1350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221389
X-RAY DIFFRACTIONr_angle_refined_deg1.6752.0181896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5535156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43124.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.76815226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.659156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021039
X-RAY DIFFRACTIONr_nbd_refined0.2130.2556
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2921
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.250
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.23
X-RAY DIFFRACTIONr_mcbond_it0.7551.5800
X-RAY DIFFRACTIONr_mcangle_it1.07921282
X-RAY DIFFRACTIONr_scbond_it1.83676
X-RAY DIFFRACTIONr_scangle_it2.3014.5614
LS refinement shellResolution: 2.7→2.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 16 -
Rwork0.302 346 -
all-362 -
obs-5169 86.6 %

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