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- PDB-5u0y: E. coli dihydropteroate synthase complexed with an 8-mercaptoguan... -

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Basic information

Entry
Database: PDB / ID: 5u0y
TitleE. coli dihydropteroate synthase complexed with an 8-mercaptoguanine derivative: [(2-amino-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl]acetic acid
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / E. coli / DHPS / complex / pterin site / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol
Similarity search - Function
Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel ...Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-7PJ / Dihydropteroate synthase
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsDennis, M.L. / Peat, T.S. / Swarbrick, J.D.
CitationJournal: Chemistry / Year: 2018
Title: 8-Mercaptoguanine Derivatives as Inhibitors of Dihydropteroate Synthase.
Authors: Dennis, M.L. / Lee, M.D. / Harjani, J.R. / Ahmed, M. / DeBono, A.J. / Pitcher, N.P. / Wang, Z.C. / Chhabra, S. / Barlow, N. / Rahmani, R. / Cleary, B. / Dolezal, O. / Hattarki, M. / Aurelio, ...Authors: Dennis, M.L. / Lee, M.D. / Harjani, J.R. / Ahmed, M. / DeBono, A.J. / Pitcher, N.P. / Wang, Z.C. / Chhabra, S. / Barlow, N. / Rahmani, R. / Cleary, B. / Dolezal, O. / Hattarki, M. / Aurelio, L. / Shonberg, J. / Graham, B. / Peat, T.S. / Baell, J.B. / Swarbrick, J.D.
History
DepositionNov 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)62,1375
Polymers61,5922
Non-polymers5453
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-21 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.936, 85.236, 84.775
Angle α, β, γ (deg.)90.00, 111.48, 90.00
Int Tables number5
Space group name H-MC121

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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 O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria)
Strain: CFT073 / ATCC 700928 / UPEC / Gene: folP, c3933 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AC14, dihydropteroate synthase
#2: Chemical ChemComp-7PJ / [(2-amino-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl]acetic acid


Mass: 241.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7N5O3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M MgCl2 25% PEG3350 0.1 M sodium HEPES, pH 7.5 apo-protein at 10 mg.mL-1 1:1 (150:150 nL) reservoir:protein Ligand soaked overnight

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.879→50 Å / Num. obs: 51039 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 27.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AJ2

1aj2


Resolution: 1.88→31.41 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.64
RfactorNum. reflection% reflection
Rfree0.2377 2548 5 %
Rwork0.2065 --
obs0.208 50950 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.88→31.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 36 340 4475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144219
X-RAY DIFFRACTIONf_angle_d1.5015706
X-RAY DIFFRACTIONf_dihedral_angle_d14.3991560
X-RAY DIFFRACTIONf_chiral_restr0.094658
X-RAY DIFFRACTIONf_plane_restr0.009749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8799-1.91610.43391710.38272540X-RAY DIFFRACTION96
1.9161-1.95520.39771360.32822687X-RAY DIFFRACTION100
1.9552-1.99770.33571290.3082698X-RAY DIFFRACTION100
1.9977-2.04410.28771370.25642695X-RAY DIFFRACTION100
2.0441-2.09520.29031330.24282697X-RAY DIFFRACTION100
2.0952-2.15190.26711480.23552654X-RAY DIFFRACTION100
2.1519-2.21520.33931260.26342716X-RAY DIFFRACTION99
2.2152-2.28670.32191490.27042683X-RAY DIFFRACTION100
2.2867-2.36840.27241320.24192694X-RAY DIFFRACTION99
2.3684-2.46310.24241400.21592671X-RAY DIFFRACTION100
2.4631-2.57520.21891340.20772696X-RAY DIFFRACTION100
2.5752-2.71090.24621300.21222696X-RAY DIFFRACTION100
2.7109-2.88060.2521400.21572717X-RAY DIFFRACTION100
2.8806-3.10290.24451360.2052687X-RAY DIFFRACTION100
3.1029-3.41480.21821390.19532732X-RAY DIFFRACTION100
3.4148-3.90810.211760.17472664X-RAY DIFFRACTION100
3.9081-4.92080.19291490.15972725X-RAY DIFFRACTION100
4.9208-31.41390.16821430.15992750X-RAY DIFFRACTION99

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