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- PDB-7reg: DfrA1 complexed with NADPH and 4'-chloro-3'-(4-(2,4-diamino-6-eth... -

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Basic information

Entry
Database: PDB / ID: 7reg
TitleDfrA1 complexed with NADPH and 4'-chloro-3'-(4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl)-[1,1'-biphenyl]-4-carboxamide (UCP1228)
ComponentsDihydrofolate reductase type 1
KeywordsOXIDOREDUCTASE / Inhibitor / complex / antifolate / DHFR
Function / homology
Function and homology information


response to methotrexate / glycine biosynthetic process / 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 domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Chem-4SI / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase type 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 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 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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)37,5517
Polymers35,1842
Non-polymers2,3675
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-28 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.860, 71.860, 119.781
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#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) / References: UniProt: P00382, dihydrofolate reductase
#2: Chemical ChemComp-4SI / 4'-chloro-3'-[(2S)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl][1,1'-biphenyl]-4-carboxamide


Mass: 419.907 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22ClN5O / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Imidazole, calcium chloride, PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 8, 2017
RadiationMonochromator: 1.54 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.77→62.31 Å / Num. obs: 35515 / % possible obs: 99.92 % / Redundancy: 2 % / Biso Wilson estimate: 23.87 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 15.37
Reflection shellResolution: 1.77→1.834 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.59 / Num. unique obs: 7017 / CC1/2: 0.863 / CC star: 0.963 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
Aimlessdata scaling
BUCCANEERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ECX

5ecx


Resolution: 1.77→43.15 Å / SU ML: 0.1709 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 20.6341
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 1664 4.69 %RANDOM
Rwork0.1902 33839 --
obs0.1917 35503 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.01 Å2
Refinement stepCycle: LAST / Resolution: 1.77→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 157 156 2787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722731
X-RAY DIFFRACTIONf_angle_d1.06663734
X-RAY DIFFRACTIONf_chiral_restr0.0682409
X-RAY DIFFRACTIONf_plane_restr0.006459
X-RAY DIFFRACTIONf_dihedral_angle_d13.091370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.820.25131470.22292760X-RAY DIFFRACTION99.93
1.82-1.880.25161380.20662802X-RAY DIFFRACTION100
1.88-1.950.24971410.22432768X-RAY DIFFRACTION99.97
1.95-2.030.2371350.18712788X-RAY DIFFRACTION100
2.03-2.120.23061230.19942820X-RAY DIFFRACTION100
2.12-2.230.26471300.18462781X-RAY DIFFRACTION100
2.23-2.370.22781470.20032796X-RAY DIFFRACTION100
2.37-2.550.22821450.19752803X-RAY DIFFRACTION100
2.55-2.810.23191550.21212785X-RAY DIFFRACTION100
2.81-3.220.24771460.19782846X-RAY DIFFRACTION99.97
3.22-4.050.21371200.17812892X-RAY DIFFRACTION99.97
4.06-43.150.16741370.17052998X-RAY DIFFRACTION99.3

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