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- PDB-6h5c: Crystal structure of DHQ1 from Salmonella typhi covalently modifi... -

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Basic information

Entry
Database: PDB / ID: 6h5c
TitleCrystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 1
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-FSQ / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description / _pdbx_entity_nonpoly.name
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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water12,665703
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-19 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.878, 43.844, 73.261
Angle α, β, γ (deg.)92.26, 93.05, 119.25
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
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 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-FSQ / (1~{S},3~{R},4~{S},5~{R})-3-methyl-3,4,5-tris(hydroxyl)cyclohexane-1-carboxylic Acid


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


Mass: 18.015 Da / Num. of mol.: 703 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 24% PEG 2000 MME, 100 mM 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: 1.14→38.14 Å / Num. obs: 150270 / % possible obs: 88.6 % / Redundancy: 1.8 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.071 / Rrim(I) all: 0.101 / Net I/σ(I): 6.3
Reflection shellResolution: 1.14→1.2 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 21721 / CC1/2: 0.61 / Rpim(I) all: 0.67 / Rrim(I) all: 0.948 / % possible all: 87.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDS1.0.5data reduction
Aimless0.5.31data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UIO

4uio


Resolution: 1.14→38.14 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.804 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.04 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18242 7885 5.2 %RANDOM
Rwork0.151 ---
obs0.15264 142383 88.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.783 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å2-1.21 Å20.65 Å2
2--0.74 Å20.57 Å2
3---0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.14→38.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 26 703 4601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194079
X-RAY DIFFRACTIONr_bond_other_d0.0020.023944
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.975561
X-RAY DIFFRACTIONr_angle_other_deg0.95839152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70924.121165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23715743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0641525
X-RAY DIFFRACTIONr_chiral_restr0.0910.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024502
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02775
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_it1.2371.1262052
X-RAY DIFFRACTIONr_mcbond_other1.2231.1252051
X-RAY DIFFRACTIONr_mcangle_it1.5631.6982571
X-RAY DIFFRACTIONr_mcangle_other1.5631.6992572
X-RAY DIFFRACTIONr_scbond_it1.6281.3842027
X-RAY DIFFRACTIONr_scbond_other1.6281.3842027
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1021.9872972
X-RAY DIFFRACTIONr_long_range_B_refined3.39115.8864674
X-RAY DIFFRACTIONr_long_range_B_other2.83914.7694474
X-RAY DIFFRACTIONr_rigid_bond_restr1.32538023
X-RAY DIFFRACTIONr_sphericity_free28.7545423
X-RAY DIFFRACTIONr_sphericity_bonded13.35758217
Refine LS restraints NCS

Ens-ID: 1 / Number: 16542 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.139→1.169 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 577 -
Rwork0.285 10395 -
obs--87.15 %

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