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- PDB-5ecx: Klebsiella pneumoniae DfrA1 complexed with NADPH and 6-ethyl-5-(3... -

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Basic information

Entry
Database: PDB / ID: 5ecx
TitleKlebsiella pneumoniae DfrA1 complexed with NADPH and 6-ethyl-5-(3-(6-(pyridin-4-yl)benzo[d][1,3]dioxol-4-yl)but-1-yn-1-yl)pyrimidine-2,4-diamine
ComponentsDehydrofolate reductase type I
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE Inhibitor / Antifolates / dfrA1 / plasmid borne resistance / OXIDOREDUCTASE-OXIDOREDUCTASE Inhibitor complex
Function / homology
Function and homology information


dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / NADP binding / cytosol
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5N1 / GLYOXYLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / dihydrofolate reductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsLombardo, M.N. / Anderson, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI104841 United States
CitationJournal: ACS Infect Dis / Year: 2016
Title: Crystal Structures of Trimethoprim-Resistant DfrA1 Rationalize Potent Inhibition by Propargyl-Linked Antifolates.
Authors: Lombardo, M.N. / G-Dayanandan, N. / Wright, D.L. / Anderson, A.C.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Data collection
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dehydrofolate reductase type I
B: Dehydrofolate reductase type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6128
Polymers35,1842
Non-polymers2,4286
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-14 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.070, 76.070, 113.929
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dehydrofolate reductase type I / DfrA1 / Dihydrofolate reductase


Mass: 17592.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: dfrA1 / Plasmid: pET-41a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / Variant (production host): De3 / References: UniProt: A4GRC7

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Non-polymers , 5 types, 80 molecules

#2: 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
#3: Chemical ChemComp-5N1 / 6-ethyl-5-[(3~{S})-3-(6-pyridin-4-yl-1,3-benzodioxol-4-yl)but-1-ynyl]pyrimidine-2,4-diamine


Mass: 387.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H21N5O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 20 mM imidazole, 300 mM calcium chloride and 15 % PEG 6,000
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5417 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.95→38.04 Å / Num. obs: 28273 / % possible obs: 99.5 % / Redundancy: 5.6 % / Rsym value: 0.053 / Net I/σ(I): 10.8
Reflection shellHighest resolution: 1.95 Å / Redundancy: 5.45 % / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementResolution: 1.95→38.035 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2656 1983 7.01 %
Rwork0.2154 --
obs0.2188 28273 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→38.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 165 74 2721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082779
X-RAY DIFFRACTIONf_angle_d1.2513801
X-RAY DIFFRACTIONf_dihedral_angle_d14.7591047
X-RAY DIFFRACTIONf_chiral_restr0.053414
X-RAY DIFFRACTIONf_plane_restr0.004468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99880.33331420.2991853X-RAY DIFFRACTION100
1.9988-2.05280.33051420.29371857X-RAY DIFFRACTION100
2.0528-2.11320.34371390.26891853X-RAY DIFFRACTION100
2.1132-2.18140.34791410.26421856X-RAY DIFFRACTION100
2.1814-2.25940.34511370.26591849X-RAY DIFFRACTION100
2.2594-2.34980.35891420.25821857X-RAY DIFFRACTION100
2.3498-2.45680.39441430.27321887X-RAY DIFFRACTION100
2.4568-2.58620.33691440.2821859X-RAY DIFFRACTION100
2.5862-2.74820.35181420.28131864X-RAY DIFFRACTION100
2.7482-2.96040.33441430.25591880X-RAY DIFFRACTION99
2.9604-3.25810.31531420.23581880X-RAY DIFFRACTION100
3.2581-3.72920.21891400.21221890X-RAY DIFFRACTION99
3.7292-4.69710.19921440.16551903X-RAY DIFFRACTION99
4.6971-38.04220.21961420.18112002X-RAY DIFFRACTION98

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