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- PDB-8b2a: Crystal structure of type I dehydroquinase from Staphylococcus au... -

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Basic information

Entry
Database: PDB / ID: 8b2a
TitleCrystal structure of type I dehydroquinase from Staphylococcus aureus inhibited by a hydroxylamine 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 type I / Type I 3-dehydroquinase / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-PVI / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.4Apr 9, 2025Group: Structure summary / Category: struct / Item: _struct.title

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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)54,6267
Polymers54,0522
Non-polymers5745
Water2,702150
1
AAA: 3-dehydroquinate dehydratase
hetero molecules

AAA: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6628
Polymers54,0522
Non-polymers6096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2540 Å2
ΔGint-52 kcal/mol
Surface area19670 Å2
MethodPISA
2
BBB: 3-dehydroquinate dehydratase
hetero molecules

BBB: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5916
Polymers54,0522
Non-polymers5384
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2240 Å2
ΔGint-31 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.382, 79.574, 83.535
Angle α, β, γ (deg.)90.000, 101.171, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11AAA-401-

HOH

21BBB-401-

HOH

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Components

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


Mass: 27026.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: aroD, SAB0760 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YWJ9, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% (w/v) PEG 3350, 0.1 M Bis-Tris-HCl, 0.2 M lithium sulfate

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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: 1.65→81.95 Å / Num. obs: 54904 / % possible obs: 98 % / Redundancy: 3.4 % / Biso Wilson estimate: 37.3495 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.017 / Rrim(I) all: 0.032 / Net I/σ(I): 19.1
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 7939 / CC1/2: 0.953 / Rpim(I) all: 0.202 / Rrim(I) all: 0.381 / % possible all: 97.7

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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: 6SFH

6sfh


Resolution: 1.65→79.701 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.959 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.122 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.255 2771 5.047 %
Rwork0.2193 52133 -
all0.221 --
obs-54904 97.769 %
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: 32.147 Å2
Baniso -1Baniso -2Baniso -3
1--1.026 Å20 Å2-1.376 Å2
2--3.294 Å20 Å2
3----1.599 Å2
Refinement stepCycle: LAST / Resolution: 1.65→79.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 33 150 3887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133832
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173670
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6395209
X-RAY DIFFRACTIONr_angle_other_deg1.3091.5828432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7445478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94125.028181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02215676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8421510
X-RAY DIFFRACTIONr_chiral_restr0.0660.2539
X-RAY DIFFRACTIONr_chiral_restr_other0.0160.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024345
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02827
X-RAY DIFFRACTIONr_nbd_refined0.2140.2764
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.23526
X-RAY DIFFRACTIONr_nbtor_refined0.1570.21881
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21874
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2137
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1840.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.225
X-RAY DIFFRACTIONr_nbd_other0.2330.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3930.217
X-RAY DIFFRACTIONr_mcbond_it2.4563.3111900
X-RAY DIFFRACTIONr_mcbond_other2.4443.311899
X-RAY DIFFRACTIONr_mcangle_it3.354.9652373
X-RAY DIFFRACTIONr_mcangle_other3.3524.9662374
X-RAY DIFFRACTIONr_scbond_it2.9673.6141930
X-RAY DIFFRACTIONr_scbond_other2.9623.5991922
X-RAY DIFFRACTIONr_scangle_it4.3955.3212833
X-RAY DIFFRACTIONr_scangle_other4.395.2972822
X-RAY DIFFRACTIONr_lrange_it5.76639.924176
X-RAY DIFFRACTIONr_lrange_other5.76739.8794161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.3191850.2933846X-RAY DIFFRACTION98.3171
1.693-1.7390.3612190.2923689X-RAY DIFFRACTION96.637
1.739-1.790.3331920.2743647X-RAY DIFFRACTION98.7905
1.79-1.8450.3761820.2653535X-RAY DIFFRACTION97.2527
1.845-1.9050.3131570.2643490X-RAY DIFFRACTION97.8535
1.905-1.9720.2631770.2563287X-RAY DIFFRACTION98.2138
1.972-2.0460.2941780.2433231X-RAY DIFFRACTION97.9316
2.046-2.130.2561530.2543125X-RAY DIFFRACTION98.4089
2.13-2.2250.2611540.2352967X-RAY DIFFRACTION98.7346
2.225-2.3330.271630.232825X-RAY DIFFRACTION97.8389
2.333-2.4590.2851520.2332701X-RAY DIFFRACTION97.5051
2.459-2.6080.251130.2122587X-RAY DIFFRACTION98.3248
2.608-2.7880.2561210.222419X-RAY DIFFRACTION98.7175
2.788-3.0110.2491060.2252270X-RAY DIFFRACTION98.0198
3.011-3.2980.2821310.2312013X-RAY DIFFRACTION96.8383
3.298-3.6870.241110.2161819X-RAY DIFFRACTION96.3555
3.687-4.2550.216980.1771607X-RAY DIFFRACTION96.6006
4.255-5.2080.198930.1641394X-RAY DIFFRACTION97.0627
5.208-7.3510.299530.2391071X-RAY DIFFRACTION96.0684
7.351-79.7010.2330.175610X-RAY DIFFRACTION95.8271

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