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- PDB-5v79: E. coli dihydropteroate synthase complexed with an 8-mercaptoguan... -

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Basic information

Entry
Database: PDB / ID: 5v79
TitleE. coli dihydropteroate synthase complexed with an 8-mercaptoguanine derivative: 2-((2-amino-9-methyl-6-oxo-6,9-dihydro-1H-purin-8-yl)thio)-N-phenylacetamide
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / 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-8Y4 / NITRATE ION / Dihydropteroate synthase
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
DepositionMar 20, 2017Deposition 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)62,3776
Polymers61,5922
Non-polymers7854
Water2,108117
1
A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2514
Polymers30,7961
Non-polymers4543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1272
Polymers30,7961
Non-polymers3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Dihydropteroate synthase
B: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,75412
Polymers123,1854
Non-polymers1,5698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area7610 Å2
ΔGint-45 kcal/mol
Surface area40510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.364, 85.621, 83.865
Angle α, β, γ (deg.)90.00, 109.67, 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-8Y4 / 2-[(2-amino-9-methyl-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl]-N-phenylacetamide


Mass: 330.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14N6O2S
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.248 M magnesium nitrate 20.3 %(w/v) PEG 8000 0.1 M tris chloride, pH 8.8 Protein at 11.1 mg.mL-1 1:1 (150:150 nL) reservoir:protein Ligand soaked into crystal (~4 h, ~2 mM)

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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: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.25→46.3 Å / Num. obs: 29678 / % possible obs: 98.4 % / Redundancy: 6.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.082 / Net I/σ(I): 11.3
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 7.32 % / Rmerge(I) obs: 1.112 / Mean I/σ(I) obs: 2.8 / Num. measured obs: 2754 / CC1/2: 0.865 / Rpim(I) all: 0.447 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AJ2

1aj2


Resolution: 2.25→46.3 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.205 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23162 1465 4.9 %RANDOM
Rwork0.19669 ---
obs0.19846 28201 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.806 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20 Å21.58 Å2
2--0.23 Å2-0 Å2
3----2.41 Å2
Refinement stepCycle: 1 / Resolution: 2.25→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 54 117 4154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194101
X-RAY DIFFRACTIONr_bond_other_d00.024033
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9785544
X-RAY DIFFRACTIONr_angle_other_deg3.72439261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5125520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.82724.524168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14815714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0061524
X-RAY DIFFRACTIONr_chiral_restr0.0760.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214678
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02890
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1963.8372095
X-RAY DIFFRACTIONr_mcbond_other2.193.8352094
X-RAY DIFFRACTIONr_mcangle_it3.5895.7322610
X-RAY DIFFRACTIONr_mcangle_other3.5895.7342611
X-RAY DIFFRACTIONr_scbond_it2.3884.1362006
X-RAY DIFFRACTIONr_scbond_other2.3884.1372001
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9816.0812929
X-RAY DIFFRACTIONr_long_range_B_refined5.75229.74472
X-RAY DIFFRACTIONr_long_range_B_other5.75129.6994473
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 100 -
Rwork0.268 2124 -
obs--99.33 %

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