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- PDB-6h5j: Crystal structure of DHQ1 from Salmonella typhi covalently modifi... -

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Basic information

Entry
Database: PDB / ID: 6h5j
TitleCrystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 4
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-FT5 / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSalmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsOtero, J.M. / Maneiro, M. / Lence, E. / Sanz-Gaitero, 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 1.2Sep 11, 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 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)27,8572
Polymers27,6811
Non-polymers1761
Water4,486249
1
A: 3-dehydroquinate dehydratase
hetero molecules

A: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7144
Polymers55,3622
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area2120 Å2
ΔGint-20 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.498, 46.598, 114.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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 typhi (bacteria) / Gene: aroD, STY1760, t1231 / Production host: Escherichia coli (E. coli) / References: UniProt: P24670, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-FT5 / (3~{R})-3,4,5-tris(hydroxyl)cyclohexane-1-carboxylic acid


Mass: 176.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.04 Å3/Da / Density % sol: 39.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 24% PEG 4000, 0.1 M citrate/phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.4→42.53 Å / Num. obs: 40717 / % possible obs: 89.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 13.4 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.017 / Rrim(I) all: 0.044 / Rsym value: 0.04 / Net I/σ(I): 10.8
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3409 / CC1/2: 0.918 / Rpim(I) all: 0.195 / Rrim(I) all: 0.437 / Rsym value: 0.387 / % possible all: 52.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALA3.3.20data scaling
MOLREP11.0.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→42.53 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.022 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17754 2040 5 %RANDOM
Rwork0.12616 ---
obs0.12869 38638 89.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.308 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0 Å20 Å2
2--0.27 Å2-0 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.4→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 12 249 2197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192052
X-RAY DIFFRACTIONr_bond_other_d0.0020.022032
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.9642802
X-RAY DIFFRACTIONr_angle_other_deg0.8783.0024675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6385274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52124.30286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5515371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.751513
X-RAY DIFFRACTIONr_chiral_restr0.1010.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022326
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.39634084
X-RAY DIFFRACTIONr_sphericity_free26.327574
X-RAY DIFFRACTIONr_sphericity_bonded9.16854216
LS refinement shellResolution: 1.4→1.476 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.265 172 -
Rwork0.18 3233 -
obs--51.86 %

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