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- PDB-3f0b: Staphylococcus aureus dihydrofolate reductase complexed with NADP... -

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Basic information

Entry
Database: PDB / ID: 3f0b
TitleStaphylococcus aureus dihydrofolate reductase complexed with NADPH and 2,4-Diamino-5-[3-(3-methoxy-5-phenylphenyl)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-53R / Chem-NDP / :
Function and homology information
Biological speciesStaphylococcus aureus RF122 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 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
DepositionOct 24, 2008Deposition 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 1.3Oct 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)19,1193
Polymers18,0161
Non-polymers1,1042
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.120, 79.120, 109.145
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-53R / 5-[(3R)-3-(5-methoxybiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine


Mass: 358.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
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: 2.07→25.35 Å / Num. all: 11715 / Num. obs: 11715 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 7.6
Reflection shellResolution: 2.07→2.15 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 3.3 / Num. unique all: 818 / Rsym value: 0.288 / % possible all: 95

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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: 2.1→25.35 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.074 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 612 5 %RANDOM
Rwork0.203 ---
all0.206 11715 --
obs0.206 11715 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 30.633 Å2 / Biso min: 14.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 75 125 1473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221416
X-RAY DIFFRACTIONr_angle_refined_deg1.4842.0371932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70424.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66415226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.948156
X-RAY DIFFRACTIONr_chiral_restr0.0940.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021065
X-RAY DIFFRACTIONr_nbd_refined0.2120.2621
X-RAY DIFFRACTIONr_nbtor_refined0.3150.2935
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.216
X-RAY DIFFRACTIONr_mcbond_it0.7531.5805
X-RAY DIFFRACTIONr_mcangle_it1.3321282
X-RAY DIFFRACTIONr_scbond_it1.6923736
X-RAY DIFFRACTIONr_scangle_it2.7254.5650
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 40 -
Rwork0.244 818 -
all-858 -
obs-11715 97.95 %

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