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- PDB-7reb: E. coli dihydrofolate reductase complexed with 5-(3-(7-(4-(aminom... -

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Basic information

Entry
Database: PDB / ID: 7reb
TitleE. coli dihydrofolate reductase complexed with 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
KeywordsOXIDOREDUCTASE / Inhibitor / antifolate / DHFR
Function / homology
Function and homology information


dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding / cytosol
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-560 / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3519
Polymers18,2631
Non-polymers1,0888
Water91951
1
A: Dihydrofolate reductase
hetero molecules

A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,70118
Polymers36,5252
Non-polymers2,17616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area3760 Å2
ΔGint-188 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.487, 66.487, 213.194
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)

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Components

#1: Protein Dihydrofolate reductase


Mass: 18262.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, folA_1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TR70, dihydrofolate reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.78 Å3/Da / Density % sol: 67.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.3-0.35 M lithium sulfate, 15-19% 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 15, 2017
Diffraction measurementDetails: 0.25 degrees, 10.85 sec, detector distance 220.00 mm
Method: \w scans
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.078 / Number: 285948
ReflectionResolution: 1.91→57.65 Å / Num. obs: 22557 / % possible obs: 97.98 % / Redundancy: 1.2 % / Biso Wilson estimate: 51.19 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 19.6
Reflection shellResolution: 1.91→1.978 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 2.26 / Num. unique obs: 2128 / CC1/2: 1 / CC star: 1 / % possible all: 96.27
Cell measurementReflection used: 285948

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rx2

1rx2


Resolution: 1.91→34.27 Å / SU ML: 0.4991 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 39.9331
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 1111 5 %RANDOM
Rwork0.2258 21111 --
obs0.227 22222 97.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.87 Å2
Refinement stepCycle: LAST / Resolution: 1.91→34.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 66 51 1397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871420
X-RAY DIFFRACTIONf_angle_d1.14851942
X-RAY DIFFRACTIONf_chiral_restr0.0608194
X-RAY DIFFRACTIONf_plane_restr0.0074251
X-RAY DIFFRACTIONf_dihedral_angle_d9.2516201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.990.53511300.56492479X-RAY DIFFRACTION95.18
1.99-2.10.43091410.48112517X-RAY DIFFRACTION95.85
2.1-2.230.35061220.32962644X-RAY DIFFRACTION99.39
2.23-2.40.38221350.33352485X-RAY DIFFRACTION93.94
2.4-2.640.29021390.26542661X-RAY DIFFRACTION99.89
2.64-3.030.26161290.25692728X-RAY DIFFRACTION99.83
3.03-3.810.26251350.22442726X-RAY DIFFRACTION99.69
3.81-34.270.21131800.18172871X-RAY DIFFRACTION98.13

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