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- PDB-8b2b: Crystal structure of type I dehydroquinase from Salmonella typhi ... -

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Basic information

Entry
Database: PDB / ID: 8b2b
TitleCrystal structure of type I dehydroquinase from Salmonella typhi inhibited by an epoxide derivative
Components3-dehydroquinate dehydratase
KeywordsLYASE / CHORISMATE BIOSYNTHETIC PROCESS / 3-DEHYDROQUINASE
Function / homology
Function and homology information


3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
3-dehydroquinate dehydratase, active site / Dehydroquinase class I active site. / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-PVI / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOtero, J.M. / Rodriguez, A. / Maneiro, M. / Lence, E. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)BFU2014-53425-P Spain
Ministerio de Ciencia e Innovacion (MCIN)BFU2017-82207-P Spain
Citation
Journal: Front Mol Biosci / Year: 2023
Title: Quinate-based ligands for irreversible inactivation of the bacterial virulence factor DHQ1 enzyme-A molecular insight.
Authors: Rodriguez, A. / Maneiro, M. / Lence, E. / Otero, J.M. / van Raaij, M.J. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C.
#1: Journal: Chemistry / Year: 2020
Title: Self-Immolation of a Bacterial Dehydratase Enzyme by its Epoxide Product.
Authors: Lence, E. / Maneiro, M. / Sanz-Gaitero, M. / van Raaij, M.J. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C.
#2: Journal: Organic Chemistry Frontiers / Year: 2019
Title: Hydroxylammonium derivatives for selective active-site lysine modification in the anti-virulence bacterial target DHQ1 enzyme
Authors: Maneiro, M. / Lence, E. / Sanz-Gaitero, M. / Otero, J.M. / van Raaij, M.J. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C.
History
DepositionSep 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: 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

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Assembly

Deposited unit
AAA: 3-dehydroquinate dehydratase
BBB: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8008
Polymers55,3622
Non-polymers4386
Water2,594144
1
AAA: 3-dehydroquinate dehydratase
hetero molecules


  • defined by author
  • 27.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)27,9004
Polymers27,6811
Non-polymers2193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: 3-dehydroquinate dehydratase
hetero molecules


  • defined by author
  • 27.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)27,9004
Polymers27,6811
Non-polymers2193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.503, 43.626, 72.372
Angle α, β, γ (deg.)84.246, 85.965, 60.935
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 3-dehydroquinate dehydratase / 3-dehydroquinase / Type I DHQase / Type I dehydroquinase / DHQ1


Mass: 27680.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Gene: aroD, STY1760, t1231 / Production host: Escherichia coli (E. coli) / References: UniProt: P24670, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-PVI / (4R,5R)-3-amino-4,5-dihydroxy-cyclohexene-1-carboxylic acid / (4~{R},5~{R})-3-amino-4,5-dihydroxy-cyclohexene-1-carboxylic acid


Mass: 173.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 12% (w/v) PEG 2000 MME, 0.1 M MES-NaOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.9→71.99 Å / Num. obs: 33302 / % possible obs: 93.5 % / Redundancy: 1.8 % / Biso Wilson estimate: 15.7791 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.056 / Rrim(I) all: 0.079 / Net I/σ(I): 6.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4751 / Rpim(I) all: 0.277 / Rrim(I) all: 0.392 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSJan 31, 2020data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CNN

4cnn


Resolution: 1.9→38.051 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.347 / SU ML: 0.212 / Cross valid method: FREE R-VALUE / ESU R: 0.226 / ESU R Free: 0.199
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2783 1729 5.256 %
Rwork0.2183 31164 -
all0.222 --
obs-32893 92.334 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.278 Å2
Baniso -1Baniso -2Baniso -3
1--3.102 Å2-0.792 Å21.487 Å2
2--2.879 Å2-2.997 Å2
3----2.799 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 26 144 4022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133972
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173875
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.6415382
X-RAY DIFFRACTIONr_angle_other_deg1.3191.5798900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4785501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18622.063189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68315706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4161526
X-RAY DIFFRACTIONr_chiral_restr0.0680.2560
X-RAY DIFFRACTIONr_chiral_restr_other0.040.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024437
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02851
X-RAY DIFFRACTIONr_nbd_refined0.2140.2861
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.23742
X-RAY DIFFRACTIONr_nbtor_refined0.1550.21923
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22030
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2177
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0570.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2730.220
X-RAY DIFFRACTIONr_nbd_other0.1860.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0620.25
X-RAY DIFFRACTIONr_mcbond_it2.6373.5062010
X-RAY DIFFRACTIONr_mcbond_other2.6353.5042009
X-RAY DIFFRACTIONr_mcangle_it3.6865.2522509
X-RAY DIFFRACTIONr_mcangle_other3.6875.2542510
X-RAY DIFFRACTIONr_scbond_it3.083.8271962
X-RAY DIFFRACTIONr_scbond_other3.083.8271962
X-RAY DIFFRACTIONr_scangle_it4.6235.6112873
X-RAY DIFFRACTIONr_scangle_other4.6235.6112874
X-RAY DIFFRACTIONr_lrange_it6.06342.3374357
X-RAY DIFFRACTIONr_lrange_other6.06142.3034336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.4381190.4732179X-RAY DIFFRACTION88.1135
1.949-2.0030.3241320.3182266X-RAY DIFFRACTION92.6942
2.003-2.0610.2881140.2942236X-RAY DIFFRACTION93.5882
2.061-2.1240.2681370.2672093X-RAY DIFFRACTION92.5695
2.124-2.1940.3161150.2462097X-RAY DIFFRACTION92.591
2.194-2.2710.443990.4281675X-RAY DIFFRACTION79.5873
2.271-2.3560.3391030.2611745X-RAY DIFFRACTION85.7939
2.356-2.4520.302790.2141947X-RAY DIFFRACTION93.9703
2.452-2.5610.251810.191819X-RAY DIFFRACTION92.955
2.561-2.6860.2861150.2071721X-RAY DIFFRACTION94.7368
2.686-2.8310.305900.1811633X-RAY DIFFRACTION94.4627
2.831-3.0030.287570.1871597X-RAY DIFFRACTION95.4414
3.003-3.2090.236760.1961482X-RAY DIFFRACTION95.058
3.209-3.4660.246710.2111377X-RAY DIFFRACTION95.5776
3.466-3.7960.281050.2051197X-RAY DIFFRACTION93.133
3.796-4.2420.207380.1771194X-RAY DIFFRACTION96.1749
4.242-4.8960.193720.1471013X-RAY DIFFRACTION96.4444
4.896-5.9890.297450.162858X-RAY DIFFRACTION96.7846
5.989-8.4410.248520.156674X-RAY DIFFRACTION97.9757
8.441-38.0510.255290.152361X-RAY DIFFRACTION97.99

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