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

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Basic information

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


dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP 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
ARGININE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TRIMETHOPRIM / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.04 Å
AuthorsErlandsen, H. / Wright, D. / Krucinska, J.
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
DepositionMay 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 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

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
C: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,89415
Polymers54,0583
Non-polymers3,83612
Water23413
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4206
Polymers18,0191
Non-polymers1,4015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3245
Polymers18,0191
Non-polymers1,3054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1494
Polymers18,0191
Non-polymers1,1303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.470, 113.397, 216.578
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules ACB

#1: Protein Dihydrofolate reductase /


Mass: 18019.340 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABQ5, dihydrofolate reductase

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Non-polymers , 5 types, 25 molecules

#2: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TOP / TRIMETHOPRIM / Trimethoprim


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


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


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.72 Å3/Da / Density % sol: 66.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 18% to 20% PEG4000 or 8000, 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: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 21, 2020
RadiationMonochromator: Double Crystal Monochromator, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 3.04→56.76 Å / Num. obs: 15680 / % possible obs: 98.7 % / Redundancy: 6 % / Biso Wilson estimate: 45.81 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 0.289 / Rpim(I) all: 0.127 / Rrim(I) all: 0.318 / Net I/σ(I): 3.9
Reflection shellResolution: 3.04→3.25 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 16148 / CC1/2: 0.345 / Rpim(I) all: 0.416 / Rrim(I) all: 0.966 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.7.4data scaling
MrBUMPphasing
REFMAC7.1.001refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PSY

4psy


Resolution: 3.04→56.76 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.822 / SU B: 23.603 / SU ML: 0.406 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2823 734 4.7 %RANDOM
Rwork0.2149 ---
obs0.2181 14913 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.68 Å2 / Biso mean: 51.221 Å2 / Biso min: 20.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å2-0 Å2
2---1.57 Å20 Å2
3----0.98 Å2
Refinement stepCycle: final / Resolution: 3.04→56.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3768 0 249 13 4030
Biso mean--58.07 30.55 -
Num. residues----474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134234
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173781
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.6455809
X-RAY DIFFRACTIONr_angle_other_deg1.1241.5828718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5735491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00922.398221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.64815640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5111526
X-RAY DIFFRACTIONr_chiral_restr0.0560.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02972
LS refinement shellResolution: 3.04→3.119 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 62 -
Rwork0.306 1126 -
all-1188 -
obs--98.34 %

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