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- PDB-7rgk: DfrA5 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)ben... -

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Basic information

Entry
Database: PDB / ID: 7rgk
TitleDfrA5 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)
ComponentsDihydrofolate reductase type 5
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibitor / complex / antifolate / DHFR / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


response to methotrexate / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to antibiotic
Similarity search - Function
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
Similarity search - Domain/homology
Chem-560 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase type 5
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsLombardo, M.N. / Wright, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Commun Biol / Year: 2022
Title: Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens.
Authors: Krucinska, J. / Lombardo, M.N. / Erlandsen, H. / Estrada, A. / Si, D. / Viswanathan, K. / Wright, D.L.
History
DepositionJul 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase type 5
B: Dihydrofolate reductase type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,79610
Polymers35,0942
Non-polymers2,7028
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-68 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.420, 99.420, 43.406
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw

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Components

#1: Protein Dihydrofolate reductase type 5 / Dihydrofolate reductase type V


Mass: 17547.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dhfrV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11731, dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-560 / 5-[(3R)-3-{7-[4-(aminomethyl)phenyl]-2H-1,3-benzodioxol-5-yl}but-1-yn-1-yl]-6-ethylpyrimidine-2,4-diamine


Mass: 415.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES, lithium sulfate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→99.42 Å / Num. obs: 22144 / % possible obs: 99.84 % / Redundancy: 1.1 % / Biso Wilson estimate: 52.39 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 14.98
Reflection shellResolution: 2.19→2.27 Å / Num. unique obs: 2220 / CC1/2: 1 / CC star: 1 / % possible all: 99.15

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RX2

1rx2


Resolution: 2.19→31.44 Å / SU ML: 0.311 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 30.9928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1066 4.82 %RANDOM
Rwork0.1843 21068 --
obs0.1865 22134 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.07 Å2
Refinement stepCycle: LAST / Resolution: 2.19→31.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 178 41 2689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912776
X-RAY DIFFRACTIONf_angle_d1.29683803
X-RAY DIFFRACTIONf_chiral_restr0.0734399
X-RAY DIFFRACTIONf_plane_restr0.0067460
X-RAY DIFFRACTIONf_dihedral_angle_d19.4189444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.290.35751430.32182594X-RAY DIFFRACTION99.31
2.29-2.410.30181150.25942649X-RAY DIFFRACTION100
2.41-2.560.32821260.25142600X-RAY DIFFRACTION100
2.56-2.760.33071040.22492641X-RAY DIFFRACTION100
2.76-3.040.27671520.23372589X-RAY DIFFRACTION100
3.04-3.480.25641570.19012611X-RAY DIFFRACTION100
3.48-4.380.17321320.16122659X-RAY DIFFRACTION100
4.38-31.440.19711370.15152725X-RAY DIFFRACTION99.79

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