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- PDB-7rud: DAHP synthase complex with trifluoropyruvate oxime -

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Basic information

Entry
Database: PDB / ID: 7rud
TitleDAHP synthase complex with trifluoropyruvate oxime
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / DAHP synthase / inhibitor / complex / LYASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / identical protein binding / cytosol / cytoplasm
Similarity search - Function
DAHP synthase, class 1 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-7QE / Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHeimhalt, M. / Mukherjee, P. / Grainger, R. / Szabla, R. / Brown, C. / Turner, R. / Junop, M.S. / Berti, P.J.
Funding support Canada, 4items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-64422 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06712 Canada
Canadian Institutes of Health Research (CIHR)MOP-166070 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)262034-2013 Canada
CitationJournal: Acs Infect Dis. / Year: 2021
Title: An Inhibitor-in-Pieces Approach to DAHP Synthase Inhibition: Potent Enzyme and Bacterial Growth Inhibition.
Authors: Heimhalt, M. / Mukherjee, P. / Grainger, R.A. / Szabla, R. / Brown, C. / Turner, R. / Junop, M.S. / Berti, P.J.
History
DepositionAug 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
B: Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
C: Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
D: Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,9377
Polymers152,4664
Non-polymers4713
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Same biological assembly as PDB accession 5CKS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13540 Å2
ΔGint-60 kcal/mol
Surface area45920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.789, 52.190, 149.800
Angle α, β, γ (deg.)90.000, 115.820, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3- ...3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3-deoxyheptonate aldolase


Mass: 38116.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: aroG, b0754, JW0737 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0AB91, 3-deoxy-7-phosphoheptulonate synthase
#2: Chemical ChemComp-7QE / (2Z)-3,3,3-trifluoro-2-(hydroxyimino)propanoic acid


Mass: 157.048 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2F3NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M trilithium citrate tetrahydrate 20% (w/v) PEG 3350 40% (v/v) 1,3-propanediol 1.8 mM trifluoropyruvate oxime

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→71.55 Å / Num. obs: 36022 / % possible obs: 97.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 41.21 Å2 / Rmerge(I) obs: 0.173 / Net I/σ(I): 5.5
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.694 / Num. unique obs: 4513

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CKS

5cks


Resolution: 2.8→71.55 Å / SU ML: 0.4655 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.4855 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2873 3065 4.86 %
Rwork0.1999 59960 -
obs0.2042 35894 89.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.7 Å2
Refinement stepCycle: LAST / Resolution: 2.8→71.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10241 0 30 58 10329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009710443
X-RAY DIFFRACTIONf_angle_d1.139414166
X-RAY DIFFRACTIONf_chiral_restr0.12341634
X-RAY DIFFRACTIONf_plane_restr0.00651856
X-RAY DIFFRACTIONf_dihedral_angle_d22.56483775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.840.40951060.31032806X-RAY DIFFRACTION89.88
2.84-2.890.3321380.28652761X-RAY DIFFRACTION89.61
2.89-2.940.43151220.27122702X-RAY DIFFRACTION89.06
2.94-2.990.40521390.27022720X-RAY DIFFRACTION88.38
2.99-3.050.35991390.27612709X-RAY DIFFRACTION88.97
3.05-3.110.37741580.26352630X-RAY DIFFRACTION88.31
3.11-3.180.32351130.24632659X-RAY DIFFRACTION86.65
3.18-3.260.32081280.25312587X-RAY DIFFRACTION83.41
3.26-3.340.35761440.24842557X-RAY DIFFRACTION85.45
3.34-3.430.3251770.25572662X-RAY DIFFRACTION89.08
3.43-3.530.3251290.22272711X-RAY DIFFRACTION88.47
3.53-3.640.31471480.20142587X-RAY DIFFRACTION85.66
3.64-3.770.3181440.19822701X-RAY DIFFRACTION88.49
3.77-3.920.27781510.18032764X-RAY DIFFRACTION92.63
3.92-4.10.29551650.18182860X-RAY DIFFRACTION93.05
4.1-4.320.26671340.16482856X-RAY DIFFRACTION92.6
4.32-4.590.20351390.1532775X-RAY DIFFRACTION92.57
4.59-4.940.22871510.15382795X-RAY DIFFRACTION91.49
4.94-5.440.25341290.16732728X-RAY DIFFRACTION89.28
5.44-6.230.29541360.18442697X-RAY DIFFRACTION88.34
6.23-7.840.26681270.17062760X-RAY DIFFRACTION90.5
7.84-71.550.17621480.15152933X-RAY DIFFRACTION95.65

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