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- PDB-5u10: E. coli dihydropteroate synthase complexed with pteroic acid -

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Basic information

Entry
Database: PDB / ID: 5u10
TitleE. coli dihydropteroate synthase complexed with pteroic acid
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
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
PHOSPHATE ION / PTEROIC ACID / Dihydropteroate synthase
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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)62,4076
Polymers61,5922
Non-polymers8154
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-48 kcal/mol
Surface area21400 Å2
2
A: Dihydropteroate synthase
B: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,81412
Polymers123,1854
Non-polymers1,6298
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area11680 Å2
ΔGint-98 kcal/mol
Surface area40190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.541, 83.868, 83.933
Angle α, β, γ (deg.)90.00, 111.03, 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PT1 / PTEROIC ACID


Mass: 312.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.134M magnesium sulfate 19.7 %w/v/ PEG8000 0.1M sodium cacodylate, pH 6.03 Protein concentration 11.1 mg.mL-1 1:1 (150:150 nL) reservoir:protein Cocrystallisation

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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: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.04→47.03 Å / Num. obs: 39630 / % possible obs: 98.9 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.4
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.898 / % possible all: 86.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AJ2

1aj2


Resolution: 2.04→47.03 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25063 1932 4.9 %RANDOM
Rwork0.20964 ---
obs0.21159 37689 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å21.14 Å2
2--1.08 Å20 Å2
3----1.99 Å2
Refinement stepCycle: 1 / Resolution: 2.04→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 56 139 4301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194229
X-RAY DIFFRACTIONr_bond_other_d00.024132
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9815719
X-RAY DIFFRACTIONr_angle_other_deg3.6739494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.455533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73724.494178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83915739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3171526
X-RAY DIFFRACTIONr_chiral_restr0.0730.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214770
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02922
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_it3.0153.6762147
X-RAY DIFFRACTIONr_mcbond_other3.0153.6752146
X-RAY DIFFRACTIONr_mcangle_it3.7275.4892675
X-RAY DIFFRACTIONr_mcangle_other3.7265.492676
X-RAY DIFFRACTIONr_scbond_it3.8653.9882082
X-RAY DIFFRACTIONr_scbond_other3.8663.9872081
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0185.8433044
X-RAY DIFFRACTIONr_long_range_B_refined5.65529.3774745
X-RAY DIFFRACTIONr_long_range_B_other5.65529.3824746
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.041→2.094 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 139 -
Rwork0.375 2682 -
obs--97.61 %

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