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- PDB-3f0q: Staphylococcus aureus dihydrofolate reductase complexed with NADP... -

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Basic information

Entry
Database: PDB / ID: 3f0q
TitleStaphylococcus aureus dihydrofolate reductase complexed with NADPH and 2,4-Diamino-5-[3-(3-methoxy-5-(2,6-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-52V / Chem-NDP / :
Function and homology information
Biological speciesStaphylococcus aureus RF122 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.08 Å
AuthorsAnderson, A.C. / Frey, K.M. / Liu, J. / Lombardo, M.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Predicting resistance mutations using protein design algorithms.
Authors: Frey, K.M. / Georgiev, I. / Donald, B.R. / 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 1.3Dec 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 1.4Apr 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
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.161, 79.161, 108.801
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-52V / 5-[(3S)-3-(5-methoxy-2',6'-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.: 121 / 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: 2.73 Å3/Da / Density % sol: 54.96 %
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: Jun 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.08→25.92 Å / Num. all: 10908 / Num. obs: 10908 / % possible obs: 87.9 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 8.6
Reflection shellResolution: 2.08→2.29 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 2.7 / Num. unique all: 782 / Rsym value: 0.143 / % possible all: 95.3

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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: 2.08→25.92 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.57 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 548 4.8 %RANDOM
Rwork0.195 ---
all0.196 10908 --
obs0.196 10908 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 191.93 Å2 / Biso mean: 20.644 Å2 / Biso min: 6.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å2-0 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.08→25.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 77 121 1471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221389
X-RAY DIFFRACTIONr_angle_refined_deg1.382.0181896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2515156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87624.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35815226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.583156
X-RAY DIFFRACTIONr_chiral_restr0.0840.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021039
X-RAY DIFFRACTIONr_nbd_refined0.2120.2604
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.217
X-RAY DIFFRACTIONr_mcbond_it0.751.5807
X-RAY DIFFRACTIONr_mcangle_it1.28321282
X-RAY DIFFRACTIONr_scbond_it1.6823685
X-RAY DIFFRACTIONr_scangle_it2.4964.5614
LS refinement shellResolution: 2.08→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 49 -
Rwork0.208 782 -
all-831 -
obs-10908 95.52 %

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