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- PDB-6xg4: X-ray structure of Escherichia coli dihydrofolate reductase L28R ... -

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Basic information

Entry
Database: PDB / ID: 6xg4
TitleX-ray structure of Escherichia coli dihydrofolate reductase L28R mutant in complex with trimethoprim
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DIHYDROFOLATE REDUCTASE / DHFR / MUTANT / COMPLEX / trimethoprim
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic 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 domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Chem-NDP / TRIMETHOPRIM / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGaszek, I.K. / Manna, M.S. / Borek, D. / Toprak, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R21GM126406 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125748 United States
CitationJournal: Nat Commun / Year: 2021
Title: A trimethoprim derivative impedes antibiotic resistance evolution.
Authors: Manna, M.S. / Tamer, Y.T. / Gaszek, I. / Poulides, N. / Ahmed, A. / Wang, X. / Toprak, F.C.R. / Woodard, D.R. / Koh, A.Y. / Williams, N.S. / Borek, D. / Atilgan, A.R. / Hulleman, J.D. / ...Authors: Manna, M.S. / Tamer, Y.T. / Gaszek, I. / Poulides, N. / Ahmed, A. / Wang, X. / Toprak, F.C.R. / Woodard, D.R. / Koh, A.Y. / Williams, N.S. / Borek, D. / Atilgan, A.R. / Hulleman, J.D. / Atilgan, C. / Tambar, U. / Toprak, E.
History
DepositionJun 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: 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)20,0565
Polymers18,8921
Non-polymers1,1634
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-13 kcal/mol
Surface area7880 Å2
Unit cell
Length a, b, c (Å)61.548, 61.548, 104.661
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydrofolate reductase


Mass: 18892.260 Da / Num. of mol.: 1 / Mutation: L28R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 MG1655 / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0ABQ4, dihydrofolate reductase

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Non-polymers , 5 types, 135 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic dihydrate (pH 5.6), 0.15 M ammonium acetate and 17.5% or 20% PEG 4000; 10 mM NADPH, 2 mM TMP was incubated with the L28R variant of DHFR overnight at 293 K
Temp details: RT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 13880 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.025 / Rrim(I) all: 0.076 / Net I/σ(I): 37.5
Reflection shellResolution: 2.1→2.12 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 334 / CC1/2: 0.672 / CC star: 0.897 / Rpim(I) all: 3.012 / Rrim(I) all: 8.94 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WT DHFR solved in the same space group

Resolution: 2.1→37.37 Å / Cor.coef. Fo:Fc: 0.908 / SU B: 10.763 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. Due to anisotropic lack of completeness, the model was first refined against all data, and the resulting model ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. Due to anisotropic lack of completeness, the model was first refined against all data, and the resulting model was refined twenty times in parallel, with each set of refinements using a different test set, until the twenty models converged. The R-free reported is the average of the twenty R-free values.
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 --FULL CROSS VALIDATION
Rwork0.2493 ---
obs0.2493 9837 70.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.96 Å2 / Biso mean: 35.198 Å2 / Biso min: 13.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å20 Å2
2---0.11 Å20 Å2
3---0.35 Å2
Refinement stepCycle: final / Resolution: 2.1→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 76 131 1478
Biso mean--27.52 31.72 -
Num. residues----159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131413
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171274
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.6511934
X-RAY DIFFRACTIONr_angle_other_deg1.1121.5832933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.565164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49821.68877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.53815219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3711511
X-RAY DIFFRACTIONr_chiral_restr0.0540.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021601
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02330
LS refinement shellResolution: 2.103→2.157 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.339 212 -
obs--21.72 %
Refinement TLS params.Method: refined / Origin x: -11.393 Å / Origin y: 22.809 Å / Origin z: 16.417 Å
111213212223313233
T0.0775 Å2-0.0178 Å2-0.0459 Å2-0.2198 Å2-0.0707 Å2--0.1881 Å2
L2.6213 °2-0.1271 °2-0.4206 °2-2.2049 °2-0.7783 °2--7.7022 °2
S0.2513 Å °0.3186 Å °-0.2622 Å °-0.133 Å °-0.0206 Å °0.1122 Å °0.4726 Å °0.0346 Å °-0.2307 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 159
2X-RAY DIFFRACTION1A301 - 303

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