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- PDB-7nae: Crystal structure of Escherichia coli dihydrofolate reductase in ... -

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Basic information

Entry
Database: PDB / ID: 7nae
TitleCrystal structure of Escherichia coli dihydrofolate reductase in complex with TRIMETHOPRIM
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / dihydrofolate reductase
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / folic acid biosynthetic process / folic acid binding / NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / folic acid biosynthetic process / folic acid binding / NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol
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
TRIMETHOPRIM / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsEstrada, A. / Wright, D. / Krucinska, J. / Erlandsen, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1 R01AI111957 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
DepositionJun 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 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 / _citation_author.identifier_ORCID / _citation_author.name
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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1377
Polymers19,3671
Non-polymers7716
Water63135
1
A: Dihydrofolate reductase
hetero molecules

A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,27514
Polymers38,7342
Non-polymers1,54112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area4880 Å2
ΔGint-191 kcal/mol
Surface area14610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.542, 65.542, 216.077
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-314-

HOH

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Components

#1: Protein Dihydrofolate reductase


Mass: 19366.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Chemical ChemComp-TOP / TRIMETHOPRIM


Mass: 290.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N4O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.46 Å3/Da / Density % sol: 64.44 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 18% to 20% PEG4K or 8K, 0.2M Ammonium Sulfate and 2mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→56.83 Å / Num. obs: 11767 / % possible obs: 96.1 % / Redundancy: 1.8 % / CC1/2: 1 / Rmerge(I) obs: 0.014 / Rpim(I) all: 0.014 / Rrim(I) all: 0.02 / Net I/σ(I): 30.2
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 5 / Num. unique obs: 1154 / CC1/2: 0.964 / Rpim(I) all: 0.162 / Rrim(I) all: 0.229 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MYM

7mym


Resolution: 2.35→56.83 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.895 / SU B: 6.409 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 593 5 %RANDOM
Rwork0.2033 ---
obs0.2062 11174 96.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 159.56 Å2 / Biso mean: 57.544 Å2 / Biso min: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å2-0 Å2
2--0.15 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 2.35→56.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 46 35 1348
Biso mean--68.44 55.6 -
Num. residues----159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131343
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171215
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.6331830
X-RAY DIFFRACTIONr_angle_other_deg1.2891.5792796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0925158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6222.32973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.61815211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.637159
X-RAY DIFFRACTIONr_chiral_restr0.070.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021498
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02306
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 43 -
Rwork0.265 823 -
all-866 -
obs--99.77 %

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