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

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Basic information

Entry
Database: PDB / ID: 3fqf
TitleStaphylococcus aureus F98Y mutant dihydrofolate reductase complexed with NADPH and 2,4-diamino-5-[3-(3,4,5-trimethoxyphenyl)pent-1-ynyl]-6-methylpyrimidine (UCP115A)
ComponentsTrimethoprim-sensitive dihydrofolate reductase
KeywordsOXIDOREDUCTASE
Function / homologyDihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / Chem-55V / Chem-NDP / :
Function and homology information
Biological speciesStaphylococcus aureus RF122 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.77 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)19,1333
Polymers18,0321
Non-polymers1,1022
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.218, 79.218, 108.746
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: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YY41, dihydrofolate reductase
#2: Chemical ChemComp-55V / 6-methyl-5-[3-methyl-3-(3,4,5-trimethoxyphenyl)but-1-yn-1-yl]pyrimidine-2,4-diamine / 2,4-Diamino-5-[3-(3,4,5-trimethoxyphenyl)pent-1-ynyl]-6-methylpyrimidine


Mass: 356.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N4O3
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 54.97 %
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: 1.77→32.72 Å / Num. obs: 17214 / % possible obs: 89.4 % / Observed criterion σ(I): 3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 1.4
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 1.1 / Num. unique all: 1374 / Rsym value: 0.167 / % 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: 1.77→32.72 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.501 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 947 5.2 %RANDOM
Rwork0.207 ---
all0.209 17214 --
obs0.209 17214 89.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.32 Å2 / Biso mean: 14.909 Å2 / Biso min: 3.09 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.77→32.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 74 184 1532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221386
X-RAY DIFFRACTIONr_bond_other_d0.0020.0225
X-RAY DIFFRACTIONr_angle_refined_deg1.3922.0191893
X-RAY DIFFRACTIONr_angle_other_deg3.31355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00724.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30815226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.949156
X-RAY DIFFRACTIONr_chiral_restr0.2420.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021032
X-RAY DIFFRACTIONr_nbd_refined0.1950.2600
X-RAY DIFFRACTIONr_nbd_other0.1910.241
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2916
X-RAY DIFFRACTIONr_nbtor_other0.0950.210
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2159
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.0960.23
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.219
X-RAY DIFFRACTIONr_mcbond_it0.641.5807
X-RAY DIFFRACTIONr_mcangle_it1.11221282
X-RAY DIFFRACTIONr_scbond_it1.453681
X-RAY DIFFRACTIONr_scangle_it2.3284.5611
LS refinement shellResolution: 1.77→1.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 85 -
Rwork0.241 1374 -
all-1459 -
obs-17214 100 %

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