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- PDB-6h5g: Crystal structure of DHQ1 from Salmonella typhi covalently modifi... -

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Basic information

Entry
Database: PDB / ID: 6h5g
TitleCrystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 3
Components3-dehydroquinate dehydratase
KeywordsLYASE / lyase activity / chorismate biosynthetic process / 3-dehydroquinase / covalent inhibitor
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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-FQZ / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsSanz-Gaitero, M. / Maneiro, M. / Lence, E. / Otero, J.M. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2014-53425-P Spain
CitationJournal: Org Chem Front / 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
DepositionJul 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country / _citation.journal_id_ISSN
Revision 1.2Aug 28, 2019Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 2024Group: 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: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8552
Polymers27,6811
Non-polymers1741
Water8,071448
1
A: 3-dehydroquinate dehydratase
hetero molecules

A: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7104
Polymers55,3622
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,-y,z1
Buried area2060 Å2
ΔGint-21 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.726, 114.632, 42.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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.: 1
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-FQZ / (1~{R},3~{S},4~{R},5~{R})-3-methyl-4,5-bis(hydroxyl)cyclohexane-1-carboxylic acid


Mass: 174.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 26% PEG 2000 MME, 100mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.04→46.73 Å / Num. obs: 109612 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 10.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.028 / Rrim(I) all: 0.068 / Net I/σ(I): 16.9
Reflection shellResolution: 1.04→1.1 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 15714 / CC1/2: 0.767 / Rpim(I) all: 0.43 / Rrim(I) all: 0.893 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimless0.5.31data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UIO

4uio


Resolution: 1.04→46.73 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.667 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.024 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14436 5426 5 %RANDOM
Rwork0.12366 ---
obs0.12471 104069 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.634 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.04→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 12 448 2396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192108
X-RAY DIFFRACTIONr_bond_other_d0.0020.022061
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9722884
X-RAY DIFFRACTIONr_angle_other_deg0.9634802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24524.36887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89915399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.391513
X-RAY DIFFRACTIONr_chiral_restr0.090.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022339
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02398
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_it0.8841.2731047
X-RAY DIFFRACTIONr_mcbond_other0.8681.2721046
X-RAY DIFFRACTIONr_mcangle_it1.1981.9211316
X-RAY DIFFRACTIONr_mcangle_other1.1981.9221317
X-RAY DIFFRACTIONr_scbond_it1.3421.5171061
X-RAY DIFFRACTIONr_scbond_other1.3421.5171061
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6632.191549
X-RAY DIFFRACTIONr_long_range_B_refined3.2418.4012506
X-RAY DIFFRACTIONr_long_range_B_other2.37316.5772357
X-RAY DIFFRACTIONr_rigid_bond_restr1.10534169
X-RAY DIFFRACTIONr_sphericity_free23.2555270
X-RAY DIFFRACTIONr_sphericity_bonded7.81654294
LS refinement shellResolution: 1.043→1.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 391 -
Rwork0.251 7543 -
obs--98.76 %

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