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- PDB-9p5i: E. coli Dihydropteroate Synthase in complex with pterin-based inh... -

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Basic information

Entry
Database: PDB / ID: 9p5i
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: 2.141 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 18, 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)60,2714
Polymers59,6902
Non-polymers5802
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-23 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.721, 94.551, 136.846
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 1 - 277 / Label seq-ID: 1 - 277

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Dihydropteroate synthase / DHPS / Dihydropteroate pyrophosphorylase


Mass: 29845.172 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-A1CG7 / 7-amino-1-methyl-3-{[(1H-tetrazol-5-yl)amino]methyl}pyrimido[4,5-c]pyridazine-4,5(1H,6H)-dione


Mass: 290.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10N10O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
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: 2.14→68.42 Å / Num. obs: 31532 / % possible obs: 98.2 % / Redundancy: 11.8 % / Biso Wilson estimate: 25.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.051 / Rrim(I) all: 0.131 / Χ2: 0.98 / Net I/σ(I): 18.1
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2357 / CC1/2: 0.722 / Rpim(I) all: 0.443 / Rrim(I) all: 0.771 / Χ2: 0.77 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
Aimlessdata scaling
Cootmodel building
REFMAC5.8.0430 (refmacat 0.4.105)phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.141→68.42 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.221 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.194 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1490 4.734 %RANDOM
Rwork0.1921 29987 --
all0.194 ---
obs-31477 97.983 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.506 Å2
Baniso -1Baniso -2Baniso -3
1--0.849 Å2-0 Å2-0 Å2
2---0.511 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.141→68.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 0 42 209 4136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124009
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.8225431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1245517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.337525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61710678
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.95410160
X-RAY DIFFRACTIONr_chiral_restr0.1040.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022963
X-RAY DIFFRACTIONr_nbd_refined0.2120.21906
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22752
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.211
X-RAY DIFFRACTIONr_mcbond_it2.462.6282074
X-RAY DIFFRACTIONr_mcangle_it3.6424.6962583
X-RAY DIFFRACTIONr_scbond_it3.6192.9161935
X-RAY DIFFRACTIONr_scangle_it5.2345.1982846
X-RAY DIFFRACTIONr_lrange_it6.66830.6456180
X-RAY DIFFRACTIONr_ncsr_local_group_10.0960.057677
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.096160.05007
12BX-RAY DIFFRACTIONLocal ncs0.096160.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.141-2.1960.251050.2441986X-RAY DIFFRACTION89.8196
2.196-2.2570.2651010.2112159X-RAY DIFFRACTION99.8233
2.257-2.3220.278930.2012059X-RAY DIFFRACTION96.2864
2.322-2.3930.2611130.1952000X-RAY DIFFRACTION99.4353
2.393-2.4720.27940.1991941X-RAY DIFFRACTION97.1824
2.472-2.5580.262800.21935X-RAY DIFFRACTION98.2927
2.558-2.6550.2811040.1971806X-RAY DIFFRACTION98.9637
2.655-2.7630.217820.1811773X-RAY DIFFRACTION97.7345
2.763-2.8860.22840.161717X-RAY DIFFRACTION99.6128
2.886-3.0260.207820.1661621X-RAY DIFFRACTION98.3256
3.026-3.190.241880.1711548X-RAY DIFFRACTION98.4949
3.19-3.3830.245520.1821519X-RAY DIFFRACTION98.8672
3.383-3.6160.244730.1791401X-RAY DIFFRACTION99.7294
3.616-3.9040.209710.1871301X-RAY DIFFRACTION99.1329
3.904-4.2760.185680.1881198X-RAY DIFFRACTION99.061
4.276-4.7780.255620.1941110X-RAY DIFFRACTION99.154
4.778-5.5130.238540.203980X-RAY DIFFRACTION98.9474
5.513-6.7410.314330.257851X-RAY DIFFRACTION99.7743
6.741-9.4870.163320.173683X-RAY DIFFRACTION99.5822
9.487-68.420.312190.219399X-RAY DIFFRACTION95.2164

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