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- PDB-3fra: Staphylococcus aureus F98Y DHFR complexed with iclaprim -

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Basic information

Entry
Database: PDB / ID: 3fra
TitleStaphylococcus aureus F98Y DHFR complexed with iclaprim
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR / NADP / One-carbon metabolism
Function / homology
Function and homology information


dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-I2H / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsOefner, C. / Dale-Glenn, E.
CitationJournal: J.Antimicrob.Chemother. / Year: 2009
Title: Increased hydrophobic interactions of iclaprim with Staphylococcus aureus dihydrofolate reductase are responsible for the increase in affinity and antibacterial activity
Authors: Oefner, C. / Bandera, M. / Haldimann, A. / Laue, H. / Schulz, H. / Mukhija, S. / Parisi, S. / Weiss, L. / Lociuro, S. / Dale, G.E.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 23, 2014Group: Non-polymer description
Revision 1.3Nov 10, 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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2593
Polymers18,1611
Non-polymers1,0982
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.200, 79.200, 108.531
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 Dihydrofolate reductase / DHFR


Mass: 18160.736 Da / Num. of mol.: 1 / Mutation: F98Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A017, dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-I2H / 5-{[(2S)-2-cyclopropyl-7,8-dimethoxy-2H-chromen-5-yl]methyl}pyrimidine-2,4-diamine


Mass: 354.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growpH: 5.5 / Details: 25% PEG 3350, 200mM NaCl, 100mM bis-Tris, pH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 8774 / Num. obs: 8774 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.35→2.5 Å / % possible all: 91.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
AMoREphasing
REFMAC5.2.0019refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.823 / SU B: 8.782 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29408 416 4.8 %RANDOM
Rwork0.22283 ---
obs0.22636 8325 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.942 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å20 Å2
2---0.07 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 74 103 1450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221387
X-RAY DIFFRACTIONr_bond_other_d00.02917
X-RAY DIFFRACTIONr_angle_refined_deg1.322.0151891
X-RAY DIFFRACTIONr_angle_other_deg0.63732238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4275156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85124.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.20815226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.157156
X-RAY DIFFRACTIONr_chiral_restr0.0390.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021471
X-RAY DIFFRACTIONr_gen_planes_other00.02269
X-RAY DIFFRACTIONr_nbd_refined0.2650.2319
X-RAY DIFFRACTIONr_nbd_other0.2810.21016
X-RAY DIFFRACTIONr_nbtor_refined0.2020.2661
X-RAY DIFFRACTIONr_nbtor_other0.0910.2761
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2510.2101
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4710.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3790.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5921002
X-RAY DIFFRACTIONr_mcbond_other0.0632316
X-RAY DIFFRACTIONr_mcangle_it0.67831280
X-RAY DIFFRACTIONr_scbond_it0.2862734
X-RAY DIFFRACTIONr_scangle_it0.4473610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.475 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.323 60 -
Rwork0.27 1069 -
obs--90.46 %

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