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- PDB-5ist: Staphylococcus aureus Dihydrofolate Reductase complexed with beta... -

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Basic information

Entry
Database: PDB / ID: 5ist
TitleStaphylococcus aureus Dihydrofolate Reductase complexed with beta-NADPH, cyclic alpha-NADPH anomer and 3'-(3-(2,4-diamino-6-ethylpyrimidin-5-yl)prop-2-yn-1-yl)-4'-methoxy-[1,1'-biphenyl]-4-carboxylic acid (UCP1106)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Dihydrofolate Reductase / NADPH / Zwitterion / Antibiotics
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-U06 / Tricyclic NADPH / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.723 Å
AuthorsAnderson, A.C. / Reeve, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI111957 United States
CitationJournal: J. Med. Chem. / Year: 2016
Title: Charged Propargyl-Linked Antifolates Reveal Mechanisms of Antifolate Resistance and Inhibit Trimethoprim-Resistant MRSA Strains Possessing Clinically Relevant Mutations.
Authors: Reeve, S.M. / Scocchera, E. / Ferreira, J.J. / G-Dayanandan, N. / Keshipeddy, S. / Wright, D.L. / Anderson, A.C.
History
DepositionMar 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2634
Polymers18,3721
Non-polymers1,8913
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.067, 79.067, 108.419
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11X-301-

HOH

DetailsMonomer according to Size Exclusion Chromatography

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Components

#1: Protein Dihydrofolate reductase / DHFR


Mass: 18371.932 Da / Num. of mol.: 1 / Mutation: H31N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folA / Plasmid: pET41a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A017, dihydrofolate reductase
#2: Chemical ChemComp-U06 / 4-[3-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]prop-2-ynyl]-4-methoxy-phenyl]benzoic acid / 3'-(3-(2,4-diamino-6-ethylpyrimidin-5-yl)prop-2-yn-1-yl)-4'-methoxy-[1,1'-biphenyl]-4-carboxylic acid / UCP1106


Mass: 402.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22N4O3
#3: Chemical ChemComp-XNP / Tricyclic NADPH


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


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 0.1 M MES pH 5.75, 0.3M sodium acetate, 17% PEG 10,000 and 20% gamma-butyrolactone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.72→31.96 Å / Num. obs: 21572 / % possible obs: 99.05 % / Redundancy: 9.3 % / Rsym value: 0.108 / Net I/σ(I): 36

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F0Q

3f0q


Resolution: 1.723→31.96 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.48
RfactorNum. reflection% reflection
Rfree0.2305 1114 5.16 %
Rwork0.1848 --
obs0.1872 21572 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.723→31.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 126 123 1520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071503
X-RAY DIFFRACTIONf_angle_d1.8722071
X-RAY DIFFRACTIONf_dihedral_angle_d17.634654
X-RAY DIFFRACTIONf_chiral_restr0.14231
X-RAY DIFFRACTIONf_plane_restr0.006252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7232-1.80160.36381330.24032508X-RAY DIFFRACTION100
1.8016-1.89660.28381180.22142534X-RAY DIFFRACTION100
1.8966-2.01540.27281340.20592532X-RAY DIFFRACTION100
2.0154-2.1710.25241610.19262510X-RAY DIFFRACTION100
2.171-2.38940.24191290.19292557X-RAY DIFFRACTION100
2.3894-2.7350.24811250.19742579X-RAY DIFFRACTION99
2.735-3.44510.22171640.18492552X-RAY DIFFRACTION99
3.4451-31.96670.18371500.15322686X-RAY DIFFRACTION96

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