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- PDB-5u13: E. coli dihydropteroate synthase complexed with an 8-mercaptoguan... -

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Basic information

Entry
Database: PDB / ID: 5u13
TitleE. coli dihydropteroate synthase complexed with an 8-mercaptoguanine derivative: 2-amino-8-{[2-(4-methoxyphenyl)-2-oxoethyl]sulfanyl}-1,7-dihydro-6H-purin-6-one
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-YH5 / Dihydropteroate synthase
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,2554
Polymers61,5922
Non-polymers6632
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-24 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.881, 84.803, 84.223
Angle α, β, γ (deg.)90.00, 110.47, 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-YH5 / 2-amino-8-{[2-(4-methoxyphenyl)-2-oxoethyl]sulfanyl}-1,9-dihydro-6H-purin-6-one


Mass: 331.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H13N5O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.066M magnesium acetate 17%w/v PEG8000 0.1M sodium cacodylate 6.3 Protein at 11.1 mg.mL-1 Cocrystallisation 1:1 (150:150 nL) reservoir:protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.951→46.676 Å / Num. obs: 45749 / % possible obs: 99.5 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.3
Reflection shellResolution: 1.951→2 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.8 / CC1/2: 0.896 / % possible all: 98.3

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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: 1.951→43.758 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.77
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 2273 4.97 %Random selection
Rwork0.187 ---
obs0.1885 45717 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.951→43.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 46 205 4317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124208
X-RAY DIFFRACTIONf_angle_d1.4015692
X-RAY DIFFRACTIONf_dihedral_angle_d18.6641559
X-RAY DIFFRACTIONf_chiral_restr0.088654
X-RAY DIFFRACTIONf_plane_restr0.007752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9507-1.99310.30331450.26292692X-RAY DIFFRACTION98
1.9931-2.03950.31511350.23282647X-RAY DIFFRACTION99
2.0395-2.09050.24521470.22692671X-RAY DIFFRACTION99
2.0905-2.1470.22671540.21522693X-RAY DIFFRACTION99
2.147-2.21010.25891440.21572714X-RAY DIFFRACTION99
2.2101-2.28150.26031600.20832702X-RAY DIFFRACTION99
2.2815-2.3630.28991350.20012693X-RAY DIFFRACTION99
2.363-2.45760.23691560.19622695X-RAY DIFFRACTION99
2.4576-2.56950.20551240.18832731X-RAY DIFFRACTION100
2.5695-2.70490.21611520.18652706X-RAY DIFFRACTION100
2.7049-2.87440.23271330.19622720X-RAY DIFFRACTION100
2.8744-3.09620.22681350.18752743X-RAY DIFFRACTION100
3.0962-3.40770.20371340.18692756X-RAY DIFFRACTION100
3.4077-3.90050.2221300.17752746X-RAY DIFFRACTION100
3.9005-4.91320.17061350.16132755X-RAY DIFFRACTION100
4.9132-43.76950.17811540.16842780X-RAY DIFFRACTION99

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