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- PDB-9dar: Structure of E. coli dihydrofolate reductase (DHFR) in an occlude... -

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Basic information

Entry
Database: PDB / ID: 9dar
TitleStructure of E. coli dihydrofolate reductase (DHFR) in an occluded conformation and in complex with cycloguanil
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / dihydrofolate reductase / occluded / cycloguanil / DHFR
Function / homology
Function and homology information


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / 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 (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Chem-1CY / CITRATE ANION / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsBerkovich, D.A. / Jez, J.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P30GM124169 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI171514 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2U01AI123394 United States
CitationJournal: Acs Infect Dis. / Year: 2025
Title: Expanding the Landscape of Dual Action Antifolate Antibacterials through 2,4-Diamino-1,6-dihydro-1,3,5-triazines.
Authors: Georgiades, J.D. / Berkovich, D.A. / McKee, S.R. / Smith, A.R. / Sankaran, B. / Flentie, K.N. / Castaneda, C.H. / Grohmann, D.G. / Rohatgi, R. / Lasky, C. / Mason, T.A. / Champine, J.E. / ...Authors: Georgiades, J.D. / Berkovich, D.A. / McKee, S.R. / Smith, A.R. / Sankaran, B. / Flentie, K.N. / Castaneda, C.H. / Grohmann, D.G. / Rohatgi, R. / Lasky, C. / Mason, T.A. / Champine, J.E. / Miller, P.A. / Mollmann, U. / Moraski, G.C. / Franzblau, S.G. / Miller, M.J. / Stallings, C.L. / Jez, J.M. / Hathaway, B.A. / Wencewicz, T.A.
History
DepositionAug 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)18,6853
Polymers18,2451
Non-polymers4412
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.076, 68.076, 212.602
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-118-

GLU

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Components

#1: Protein Dihydrofolate reductase


Mass: 18244.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, c0058 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ5, dihydrofolate reductase
#2: Chemical ChemComp-1CY / 1-(4-chlorophenyl)-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine / Cycloguanil


Mass: 251.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14ClN5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor, antagonist*YM
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.9 Å3/Da / Density % sol: 68.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium citrate dibasic, 20% (w/v) PEG 3350

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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: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.17→34.5 Å / Num. obs: 12722 / % possible obs: 94.2 % / Redundancy: 23 % / CC1/2: 0.999 / Rpim(I) all: 0.025 / Net I/σ(I): 16.6
Reflection shellResolution: 2.17→2.38 Å / Redundancy: 19.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 636 / CC1/2: 0.768 / Rpim(I) all: 0.438 / % possible all: 56.3

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→34.49 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 590 4.64 %
Rwork0.2096 --
obs0.2116 12720 78.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→34.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 30 48 1362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091365
X-RAY DIFFRACTIONf_angle_d1.2921866
X-RAY DIFFRACTIONf_dihedral_angle_d10.048192
X-RAY DIFFRACTIONf_chiral_restr0.066194
X-RAY DIFFRACTIONf_plane_restr0.009246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.390.3064260.2874647X-RAY DIFFRACTION17
2.39-2.730.32051570.28323534X-RAY DIFFRACTION92
2.73-3.440.26011990.23573833X-RAY DIFFRACTION100
3.44-34.490.23612080.18344116X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.86690.8441.75423.2162-0.03236.03420.1861-0.09040.2009-0.28470.3022-0.3449-0.03331.3137-0.33610.4174-0.00580.02090.5856-0.15430.5319-19.723221.7327-6.9764
22.08911.28982.20081.86690.13654.89520.01250.05760.14970.0167-0.0063-0.0191-0.29290.5831-0.02750.3201-0.0080.0680.3945-0.14320.3738-17.841629.40773.5308
31.42821.13022.09452.1945-0.24296.16650.28520.0854-0.38180.2207-0.0139-0.15311.00440.4948-0.34240.47380.0644-0.0230.4091-0.08790.4452-22.578915.7944-3.5257
43.344-0.09791.03092.26650.01196.82320.28240.2302-0.5707-0.18-0.01450.04320.2830.1175-0.16990.2987-0.0226-0.06570.2993-0.07580.4601-30.637720.4055-11.7779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 129 )
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 159 )

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