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- PDB-5u12: E. coli dihydropteroate synthase complexed with an 8-mercaptoguan... -

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Basic information

Entry
Database: PDB / ID: 5u12
TitleE. coli dihydropteroate synthase complexed with an 8-mercaptoguanine derivative: 2-azanyl-8-[(2-fluorophenyl)methylsulfanyl]-1,9-dihydropurin-6-one
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / E. coli / DHPS / complex / pterin site
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-5RU / Dihydropteroate synthase
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.839 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)62,1754
Polymers61,5922
Non-polymers5832
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-23 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.887, 84.546, 84.145
Angle α, β, γ (deg.)90.00, 109.87, 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-5RU / 2-azanyl-8-[(2-fluorophenyl)methylsulfanyl]-1,9-dihydropurin-6-one


Mass: 291.304 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10FN5OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 52.76 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.147M magnesium acetate 27.1% [w/v] MPEG 5000 0.1M tris chloride, pH 8.8 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 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.839→46.57 Å / Num. obs: 54783 / % possible obs: 99.7 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.6
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.8 / CC1/2: 0.872 / % possible all: 97

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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: 1.839→45.089 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 2794 5.1 %Random selection
Rwork0.1797 ---
obs0.181 54764 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.839→45.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4098 0 40 245 4383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014230
X-RAY DIFFRACTIONf_angle_d1.2845720
X-RAY DIFFRACTIONf_dihedral_angle_d18.7811565
X-RAY DIFFRACTIONf_chiral_restr0.084657
X-RAY DIFFRACTIONf_plane_restr0.006741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8389-1.87060.28121500.2462526X-RAY DIFFRACTION97
1.8706-1.90460.25771370.22362552X-RAY DIFFRACTION100
1.9046-1.94130.24351240.21022622X-RAY DIFFRACTION100
1.9413-1.98090.26451240.20312575X-RAY DIFFRACTION100
1.9809-2.0240.23761530.20112601X-RAY DIFFRACTION100
2.024-2.0710.27691420.20112578X-RAY DIFFRACTION100
2.071-2.12280.24191490.18562606X-RAY DIFFRACTION100
2.1228-2.18020.23281440.19112591X-RAY DIFFRACTION100
2.1802-2.24440.23791480.18772571X-RAY DIFFRACTION100
2.2444-2.31680.22311200.19382613X-RAY DIFFRACTION100
2.3168-2.39960.24371390.18612605X-RAY DIFFRACTION100
2.3996-2.49570.22951230.18322602X-RAY DIFFRACTION100
2.4957-2.60930.21911320.1792622X-RAY DIFFRACTION100
2.6093-2.74680.18051230.17842619X-RAY DIFFRACTION100
2.7468-2.91890.21831380.18022612X-RAY DIFFRACTION100
2.9189-3.14420.2121410.18122613X-RAY DIFFRACTION100
3.1442-3.46050.19461640.17562566X-RAY DIFFRACTION100
3.4605-3.9610.1721420.16112631X-RAY DIFFRACTION100
3.961-4.98940.17761520.16172621X-RAY DIFFRACTION100
4.9894-45.1030.17491490.17532644X-RAY DIFFRACTION99

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