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- PDB-7rue: DAHP synthase complexed with trifluoropyruvate semicarbazone -

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Basic information

Entry
Database: PDB / ID: 7rue
TitleDAHP synthase complexed with trifluoropyruvate semicarbazone
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-7QH / : / Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)2017-06712 Canada
Canadian Institutes of Health Research (CIHR)MOP-89903 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)153,48212
Polymers152,4664
Non-polymers1,0168
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Same biological assembly evidence as PDB: 5CKS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-76 kcal/mol
Surface area45110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.281, 53.200, 150.790
Angle α, β, γ (deg.)90.000, 116.010, 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-7QH / (2E)-2-(2-carbamoylhydrazinylidene)-3,3,3-trifluoropropanoic acid


Mass: 199.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4F3N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M trilithium citrate tetrahydrate 20% (w/v) PEG 3350 1 M MnCl2 2 mM trifluoropyruvate semicarbazone

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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: 2.5→72.02 Å / Num. obs: 52544 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 37.23 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.073 / Rrim(I) all: 0.133 / Net I/av σ(I): 6.8 / Net I/σ(I): 6.8
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4524 / CC1/2: 0.801 / Rpim(I) all: 0.397 / Rrim(I) all: 0.329 / % possible all: 99.9

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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: 2.5→50.21 Å / SU ML: 0.3719 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7414 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2633 4900 5.05 %
Rwork0.2012 92188 -
obs0.2044 52507 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.79 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10118 0 56 122 10296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009710340
X-RAY DIFFRACTIONf_angle_d1.115814035
X-RAY DIFFRACTIONf_chiral_restr0.14221632
X-RAY DIFFRACTIONf_plane_restr0.01441829
X-RAY DIFFRACTIONf_dihedral_angle_d21.24113695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.36731420.3193199X-RAY DIFFRACTION95.54
2.53-2.560.3261700.29743037X-RAY DIFFRACTION97.15
2.56-2.590.33611910.2893074X-RAY DIFFRACTION96.63
2.59-2.620.331510.27813089X-RAY DIFFRACTION96.75
2.62-2.660.35611880.29183226X-RAY DIFFRACTION97.32
2.66-2.690.39511300.2713033X-RAY DIFFRACTION96.26
2.69-2.730.34561690.27343090X-RAY DIFFRACTION95.82
2.73-2.770.38361780.27653106X-RAY DIFFRACTION96.08
2.77-2.820.36121720.2753094X-RAY DIFFRACTION96.17
2.82-2.860.36691710.27773026X-RAY DIFFRACTION96.09
2.86-2.910.38321530.27583102X-RAY DIFFRACTION96.59
2.91-2.960.32032070.26543070X-RAY DIFFRACTION94.74
2.96-3.020.34741580.25113021X-RAY DIFFRACTION94.61
3.02-3.080.28481710.25393027X-RAY DIFFRACTION94.62
3.08-3.150.31521800.2482995X-RAY DIFFRACTION93.44
3.15-3.220.34291260.23952942X-RAY DIFFRACTION91.34
3.22-3.30.33121500.24152954X-RAY DIFFRACTION89.87
3.3-3.390.28941540.22462942X-RAY DIFFRACTION92.14
3.39-3.490.29941690.21313064X-RAY DIFFRACTION95.82
3.49-3.610.22021600.19643075X-RAY DIFFRACTION95.2
3.61-3.730.28071670.18843058X-RAY DIFFRACTION95.61
3.73-3.880.1931820.17313147X-RAY DIFFRACTION97.71
3.88-4.060.22541410.16273148X-RAY DIFFRACTION97.63
4.06-4.270.21631460.14853111X-RAY DIFFRACTION96.85
4.27-4.540.19351860.13463140X-RAY DIFFRACTION97.88
4.54-4.890.1771540.13623127X-RAY DIFFRACTION96.19
4.89-5.380.18821700.14853052X-RAY DIFFRACTION95.52
5.38-6.160.21381410.16742879X-RAY DIFFRACTION89.8
6.16-7.760.20371950.16723129X-RAY DIFFRACTION97.31
7.76-50.210.22411280.15483231X-RAY DIFFRACTION99.29

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