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- PDB-5jg0: Staphylococcus aureus Dihydrofolate Reductase complexed with beta... -

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Basic information

Entry
Database: PDB / ID: 5jg0
TitleStaphylococcus aureus Dihydrofolate Reductase complexed with beta-NADPH and UCP1191
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Dihydrofolate Reductase / NADPH / Zwitterion / Antibiotics
Function / homology
Function and homology information


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-UC9 / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.879 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: Cell Chem Biol / Year: 2016
Title: MRSA Isolates from United States Hospitals Carry dfrG and dfrK Resistance Genes and Succumb to Propargyl-Linked Antifolates.
Authors: Reeve, S.M. / Scocchera, E.W. / G-Dayanadan, N. / Keshipeddy, S. / Krucinska, J. / Hajian, B. / Ferreira, J. / Nailor, M. / Aeschlimann, J. / Wright, D.L. / Anderson, A.C.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)19,1893
Polymers18,0161
Non-polymers1,1742
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.875, 78.875, 106.431
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: 18015.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folA / Plasmid: pET41-a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A017, dihydrofolate reductase
#2: Chemical ChemComp-UC9 / 4-{6-[(2S)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-2H-1,3-benzodioxol-4-yl}benzoic acid


Mass: 430.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22N4O4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M MES, pH 5.0, 0.3M sodium acetate, 17% PEG 10,000, 12.5% gamma-butrylactone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.22 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.22 Å / Relative weight: 1
ReflectionResolution: 1.879→39.44 Å / Num. obs: 16498 / % possible obs: 99.75 % / Redundancy: 16.7 % / Rsym value: 0.107 / Net I/σ(I): 41.2
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 5.52 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.879→39.438 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 1650 10 %
Rwork0.1765 --
obs0.1806 16498 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.879→39.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 80 69 1422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071434
X-RAY DIFFRACTIONf_angle_d1.2381967
X-RAY DIFFRACTIONf_dihedral_angle_d15.032544
X-RAY DIFFRACTIONf_chiral_restr0.053216
X-RAY DIFFRACTIONf_plane_restr0.005245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8794-1.93470.2521300.19581172X-RAY DIFFRACTION97
1.9347-1.99710.25171330.18861200X-RAY DIFFRACTION100
1.9971-2.06850.24531370.18741228X-RAY DIFFRACTION100
2.0685-2.15130.23341330.17991198X-RAY DIFFRACTION100
2.1513-2.24920.21941360.18421227X-RAY DIFFRACTION100
2.2492-2.36780.25251370.19221222X-RAY DIFFRACTION100
2.3678-2.51610.22731340.19831214X-RAY DIFFRACTION100
2.5161-2.71030.24511380.19881243X-RAY DIFFRACTION100
2.7103-2.9830.26131380.19611237X-RAY DIFFRACTION100
2.983-3.41440.21881390.18271258X-RAY DIFFRACTION100
3.4144-4.3010.20241420.15181269X-RAY DIFFRACTION100
4.301-39.44620.17671530.16151380X-RAY DIFFRACTION100

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