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- PDB-3f0x: Staphylococcus aureus F98Y mutant dihydrofolate reductase complex... -

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Basic information

Entry
Database: PDB / ID: 3f0x
TitleStaphylococcus aureus F98Y mutant 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: 2.6 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 27, 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 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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)19,1633
Polymers18,0321
Non-polymers1,1322
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.048, 79.048, 108.727
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: 18031.557 Da / Num. of mol.: 1 / Mutation: F98Y
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.72 Å3/Da / Density % sol: 54.77 %
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: 2.6→39.53 Å / Num. all: 5893 / Num. obs: 5893 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 4.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 4.3 / Num. unique all: 208 / Rsym value: 0.286 / % possible all: 85.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
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: 2.6→39.53 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.876 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 11.194 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.319 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 293 4.7 %RANDOM
Rwork0.212 ---
all0.214 5893 --
obs0.214 5893 93.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.75 Å2 / Biso mean: 15.908 Å2 / Biso min: 2 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: 2.6→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 77 8 1359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221442
X-RAY DIFFRACTIONr_angle_refined_deg1.6272.0591978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4475156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86724.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.94815226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.941156
X-RAY DIFFRACTIONr_chiral_restr0.1110.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021062
X-RAY DIFFRACTIONr_nbd_refined0.2030.2603
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2948
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.22
X-RAY DIFFRACTIONr_mcbond_it0.5891.5801
X-RAY DIFFRACTIONr_mcangle_it1.07621282
X-RAY DIFFRACTIONr_scbond_it1.2583755
X-RAY DIFFRACTIONr_scangle_it1.864.5696
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 7 -
Rwork0.299 208 -
all-215 -
obs-5893 85.3 %

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