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- PDB-5u0w: E. coli dihydropteroate synthase complexed with 9-methylguanine -

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Basic information

Entry
Database: PDB / ID: 5u0w
TitleE. coli dihydropteroate synthase complexed with 9-methylguanine
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
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
9-METHYLGUANINE / ACETIC ACID / Dihydropteroate synthase
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.968 Å
AuthorsChhabra, S. / Dennis, 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)61,9835
Polymers61,5922
Non-polymers3903
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-14 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.542, 85.513, 84.281
Angle α, β, γ (deg.)90.00, 111.52, 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-9MG / 9-METHYLGUANINE


Mass: 165.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H7N5O
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 52.69 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 16.9% PEG8000 0.1 M sodium cacodylate, pH 6.0 0.143M MgNO3 Protein at 15 mg.mL-1

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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: Oct 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.968→19.771 Å / Num. obs: 44542 / % possible obs: 99.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.8

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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: 1.968→19.771 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 2212 5.03 %
Rwork0.1875 --
obs0.1892 43966 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.968→19.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 28 241 4336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094201
X-RAY DIFFRACTIONf_angle_d1.1735688
X-RAY DIFFRACTIONf_dihedral_angle_d15.2751554
X-RAY DIFFRACTIONf_chiral_restr0.052658
X-RAY DIFFRACTIONf_plane_restr0.004739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9685-2.01120.3779950.30442033X-RAY DIFFRACTION76
2.0112-2.0580.28151250.24252643X-RAY DIFFRACTION99
2.058-2.10940.30641670.22992596X-RAY DIFFRACTION100
2.1094-2.16630.27231400.22162632X-RAY DIFFRACTION100
2.1663-2.230.22651220.21772644X-RAY DIFFRACTION100
2.23-2.30190.28231430.2242634X-RAY DIFFRACTION100
2.3019-2.3840.27071530.21372647X-RAY DIFFRACTION100
2.384-2.47930.29631270.20692651X-RAY DIFFRACTION100
2.4793-2.59190.28471570.20772622X-RAY DIFFRACTION100
2.5919-2.72820.25491360.20842634X-RAY DIFFRACTION100
2.7282-2.89870.26321520.21422646X-RAY DIFFRACTION100
2.8987-3.12170.22881420.19962652X-RAY DIFFRACTION100
3.1217-3.43430.22221480.18712654X-RAY DIFFRACTION100
3.4343-3.92790.18921300.16662660X-RAY DIFFRACTION100
3.9279-4.9360.19051350.14622696X-RAY DIFFRACTION100
4.936-19.77240.14121400.15842710X-RAY DIFFRACTION100

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