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- PDB-9p4a: E. coli Dihydropteroate Synthase in complex with pterin-based inh... -

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Basic information

Entry
Database: PDB / ID: 9p4a
TitleE. coli Dihydropteroate Synthase in complex with pterin-based inhibitor
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / Inhibitor
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / response to xenobiotic stimulus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like
Similarity search - Domain/homology
: / Dihydropteroate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSnoke, H.E. / Reeve, S.M. / Lee, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI136803 United States
CitationJournal: Acs Infect Dis. / Year: 2025
Title: Development of Pyrimido Pyridazine Analogs through Increased Whole Cell Target Engagement of the Dihydropteroate Synthase Pterin Binding Site in Gram-Negative Bacteria.
Authors: Snoke, H.E. / Reeve, S.M. / Dharuman, S. / Wallace, M.J. / Loudon, V.C. / Zhao, Y. / Bowling, J.J. / Murphy, P.A. / Waddell, B. / Lee, R.B. / Bulitta, J.B. / Lee, R.E.
History
DepositionJun 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydropteroate synthase
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0954
Polymers61,5922
Non-polymers5022
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-24 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.600, 84.807, 82.181
Angle α, β, γ (deg.)90.000, 102.879, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Dihydropteroate synthase / DHPS / Dihydropteroate pyrophosphorylase


Mass: 30796.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folP, dhpS, b3177, JW3144 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AC13, dihydropteroate synthase
#2: Chemical ChemComp-A1CG3 / (2S)-2-(7-amino-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)propanoic acid


Mass: 251.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 50 mM Tris, 32-50% Ammonium Sulfate / PH range: 8.0-8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 10646 / % possible obs: 85.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 57.02 Å2 / CC1/2: 0.943 / CC star: 0.985 / Rpim(I) all: 0.08 / Rrim(I) all: 0.161 / Χ2: 1.707 / Net I/σ(I): 13.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.01 / Num. unique obs: 588 / CC1/2: 0.815 / CC star: 0.948 / Rpim(I) all: 0.361 / Rrim(I) all: 0.761 / Χ2: 0.823 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→38 Å / SU ML: 0.5914 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.1751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3371 977 9.99 %
Rwork0.2325 8802 -
obs0.243 9779 82.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.56 Å2
Refinement stepCycle: LAST / Resolution: 3→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3797 0 36 4 3837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893890
X-RAY DIFFRACTIONf_angle_d1.08375264
X-RAY DIFFRACTIONf_chiral_restr0.053619
X-RAY DIFFRACTIONf_plane_restr0.0088678
X-RAY DIFFRACTIONf_dihedral_angle_d17.50561410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.45591550.31921461X-RAY DIFFRACTION97.06
3.16-3.360.33241690.24771463X-RAY DIFFRACTION96.91
3.36-3.610.43291200.32521074X-RAY DIFFRACTION71.58
3.62-3.980.3462630.2809576X-RAY DIFFRACTION37.99
3.98-4.550.33431570.20241406X-RAY DIFFRACTION93.71
4.55-5.730.29511590.20471415X-RAY DIFFRACTION93.41
5.73-380.2931540.19471407X-RAY DIFFRACTION90.34

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