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- PDB-6h5d: Crystal structure of DHQ1 from Salmonella typhi covalently modifi... -

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Basic information

Entry
Database: PDB / ID: 6h5d
TitleCrystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 2
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 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-WPL / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSalmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7424
Polymers55,3622
Non-polymers3802
Water13,673759
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-22 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.219, 44.057, 84.600
Angle α, β, γ (deg.)90.00, 95.25, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 252 / Label seq-ID: 1 - 252

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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 typhi (bacteria) / Gene: aroD, STY1760, t1231 / Production host: Escherichia coli (E. coli) / References: UniProt: P24670, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-WPL / (1~{S},3~{S},4~{R},5~{R})-3-methyl-1,4,5-tris(hydroxyl)cyclohexane-1-carboxylic acid


Mass: 190.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / Source method: isolated from a natural source / Formula: H2O
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: 2.02 Å3/Da / Density % sol: 39.07 %
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: 1.25→59.97 Å / Num. obs: 115498 / % possible obs: 94.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 7.9 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.069 / Rrim(I) all: 0.1 / Net I/σ(I): 8.5
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5854 / CC1/2: 0.538 / Rpim(I) all: 0.568 / Rrim(I) all: 0.824 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UIO

4uio


Resolution: 1.25→59.97 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.388 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.055 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19973 5737 5 %RANDOM
Rwork0.15793 ---
obs0.16 109028 93.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.035 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.02 Å2
2--0.69 Å20 Å2
3----0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.25→59.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 26 759 4657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194186
X-RAY DIFFRACTIONr_bond_other_d0.0020.024051
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.975738
X-RAY DIFFRACTIONr_angle_other_deg0.98539427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6115574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.61624.425174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71815770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7271525
X-RAY DIFFRACTIONr_chiral_restr0.0960.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024665
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02797
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_it1.0551.0482088
X-RAY DIFFRACTIONr_mcbond_other1.0551.0482087
X-RAY DIFFRACTIONr_mcangle_it1.3721.5782625
X-RAY DIFFRACTIONr_mcangle_other1.3721.5782626
X-RAY DIFFRACTIONr_scbond_it1.3691.282098
X-RAY DIFFRACTIONr_scbond_other1.3691.282098
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6851.8313077
X-RAY DIFFRACTIONr_long_range_B_refined3.40314.8214879
X-RAY DIFFRACTIONr_long_range_B_other2.78413.7064673
X-RAY DIFFRACTIONr_rigid_bond_restr1.14638237
X-RAY DIFFRACTIONr_sphericity_free27.4995470
X-RAY DIFFRACTIONr_sphericity_bonded7.54258422
Refine LS restraints NCS

Ens-ID: 1 / Number: 16462 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 435 -
Rwork0.293 8247 -
obs--96.18 %

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