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

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Basic information

Entry
Database: PDB / ID: 3fqo
TitleStaphylococcus aureus F98Y mutant dihydrofolate reductase complexed with NADPH and 2,4-diamino-5-[3-(2,5-dimethoxyphenyl)prop-1-ynyl]-6-ethylpyrimidine (UCP120B)
ComponentsTrimethoprim-sensitive dihydrofolate reductase
KeywordsOXIDOREDUCTASE
Function / homologyDihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / Chem-N22 / Chem-NDP / :
Function and homology information
Biological speciesStaphylococcus aureus RF122 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.09 Å
AuthorsAnderson, A.C. / Frey, K.M. / Liu, J. / Lombardo, M.N.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structures of wild-type and mutant methicillin-resistant Staphylococcus aureus dihydrofolate reductase reveal an alternate conformation of NADPH that may be linked to trimethoprim resistance.
Authors: Frey, K.M. / Liu, J. / Lombardo, M.N. / Bolstad, D.B. / Wright, D.L. / Anderson, A.C.
History
DepositionJan 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2013Group: Non-polymer description
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 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
A: Trimethoprim-sensitive dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0893
Polymers18,0321
Non-polymers1,0582
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.866, 78.866, 107.825
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) / Strain: RF122 / ET3-1 / Gene: dfrB, SAB1281c / 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-N22 / 5-[3-(2,5-dimethoxyphenyl)prop-1-yn-1-yl]-6-ethylpyrimidine-2,4-diamine


Mass: 312.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 10000, 150mM Sodium acetate, 100mM 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: Apr 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.09→42.33 Å / Num. obs: 11685 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 9.4 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 5
Reflection shellResolution: 2.09→2.18 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.8 / Num. unique all: 838 / Rsym value: 0.406 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
Cootmodel building
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: Sa F98Y DHFR bound to Folate and NADPH (Dale et al., J.Mol.Biol. 1997, structure not deposited in the PDB)

Resolution: 2.09→42.33 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.232 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 608 4.9 %RANDOM
Rwork0.216 ---
all0.218 11685 --
obs0.218 11685 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.56 Å2 / Biso mean: 30.258 Å2 / Biso min: 5.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.09→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 71 65 1410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221435
X-RAY DIFFRACTIONr_angle_refined_deg1.3952.0541966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0995156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26324.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62615226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.202156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021053
X-RAY DIFFRACTIONr_nbd_refined0.1840.2621
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2958
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.28
X-RAY DIFFRACTIONr_mcbond_it0.5831.5806
X-RAY DIFFRACTIONr_mcangle_it1.03721282
X-RAY DIFFRACTIONr_scbond_it1.1893739
X-RAY DIFFRACTIONr_scangle_it1.914.5684
LS refinement shellResolution: 2.09→2.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 43 -
Rwork0.27 838 -
all-881 -
obs-11685 100 %

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