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- PDB-7rgj: DfrA1 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)ben... -

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Basic information

Entry
Database: PDB / ID: 7rgj
TitleDfrA1 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 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibitor / complex / antifolate / DHFR / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


response to methotrexate / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / 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 / Chem-8MU / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase type 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsLombardo, M.N. / Wright, D.L.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
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

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase type 1
B: Dihydrofolate reductase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9979
Polymers35,1842
Non-polymers2,8137
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.279, 72.279, 120.148
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Components on special symmetry positions
IDModelComponents
11B-204-

8MU

21B-204-

8MU

31B-204-

8MU

41B-204-

8MU

51B-204-

8MU

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydrofolate reductase type 1 / Dihydrofolate reductase type I / Trimethoprim resistance protein


Mass: 17592.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dhfrI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00382, dihydrofolate reductase

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Non-polymers , 5 types, 215 molecules

#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-8MU / 5-[(3S)-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: 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.: 1 / Source method: obtained synthetically / Formula: C24H25N5O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Imidazole, calcium chloride, PEG 6,000

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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: Jun 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→62.67 Å / Num. obs: 65686 / % possible obs: 99.27 % / Redundancy: 1.1 % / Biso Wilson estimate: 23.93 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 20.35
Reflection shellResolution: 1.44→1.493 Å / Num. unique obs: 6480 / CC1/2: 1 / CC star: 1 / % possible all: 99.4

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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: 5ECX

5ecx


Resolution: 1.44→30.29 Å / SU ML: 0.1536 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 22.6337
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3320 5.05 %RANDOM
Rwork0.1983 62361 --
obs0.1997 65681 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.3 Å2
Refinement stepCycle: LAST / Resolution: 1.44→30.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2464 0 191 208 2863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682849
X-RAY DIFFRACTIONf_angle_d1.09763906
X-RAY DIFFRACTIONf_chiral_restr0.0842418
X-RAY DIFFRACTIONf_plane_restr0.0057479
X-RAY DIFFRACTIONf_dihedral_angle_d14.5936431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.460.29451000.27272583X-RAY DIFFRACTION98.57
1.46-1.480.29861340.24662580X-RAY DIFFRACTION100
1.48-1.510.25991440.23492606X-RAY DIFFRACTION100
1.51-1.530.23621430.22562531X-RAY DIFFRACTION100
1.53-1.560.25911450.21752596X-RAY DIFFRACTION100
1.56-1.590.21081460.21142554X-RAY DIFFRACTION100
1.59-1.620.26771280.21882616X-RAY DIFFRACTION100
1.62-1.650.22281400.20422626X-RAY DIFFRACTION99.96
1.65-1.690.24231350.20112595X-RAY DIFFRACTION100
1.69-1.730.24911200.20382581X-RAY DIFFRACTION100
1.73-1.770.26011660.21192576X-RAY DIFFRACTION100
1.77-1.820.20681530.19762579X-RAY DIFFRACTION100
1.82-1.870.22491290.20572609X-RAY DIFFRACTION100
1.87-1.930.22111410.19862593X-RAY DIFFRACTION100
1.93-20.2461510.20232611X-RAY DIFFRACTION100
2-2.080.24421330.19412596X-RAY DIFFRACTION100
2.08-2.170.22841340.20032638X-RAY DIFFRACTION100
2.17-2.290.21991220.1932628X-RAY DIFFRACTION99.96
2.29-2.430.2181820.20292590X-RAY DIFFRACTION100
2.43-2.620.21921480.20522618X-RAY DIFFRACTION100
2.62-2.880.24171400.21442653X-RAY DIFFRACTION99.93
2.88-3.30.21341060.19762715X-RAY DIFFRACTION99.89
3.3-4.150.21431400.17832643X-RAY DIFFRACTION98.76
4.16-30.290.2291400.19432444X-RAY DIFFRACTION86.89

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