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- PDB-2xda: STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLE... -

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Basic information

Entry
Database: PDB / ID: 2xda
TitleSTRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (4R,6R,7S)-2-(2-Cyclopropyl)ethyl-4,6,7- trihydroxy-4,5,6,7-tetrahydrobenzo(b)thiophene-4-carboxylic acid
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / AROMATIC AMINO ACID BIOSYNTHESIS
Function / homology
Function and homology information


quinate catabolic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Dehydroquinase, class II / Dehydroquinase, class II, conserved site / Dehydroquinase class II signature. / Dehydroquinase, class II / Dehydroquinase, class II superfamily / Dehydroquinase class II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-JPS / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPaz, S. / Tizon, L. / Otero, J.M. / Llamas-Saiz, A.L. / Fox, G.C. / van Raaij, M.J. / Lamb, H. / Hawkins, A.R. / Castedo, L. / Gonzalez-Bello, C.
CitationJournal: ChemMedChem / Year: 2011
Title: Tetrahydrobenzothiophene derivatives: conformationally restricted inhibitors of type II dehydroquinase.
Authors: Paz, S. / Tizon, L. / Otero, J.M. / Llamas-Saiz, A.L. / Fox, G.C. / van Raaij, M.J. / Lamb, H. / Hawkins, A.R. / Lapthorn, A.J. / Castedo, L. / Gonzalez-Bello, C.
History
DepositionApr 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references / Version format compliance
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)18,7982
Polymers18,4991
Non-polymers2981
Water1,982110
1
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)225,57124
Polymers221,99112
Non-polymers3,58012
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation8_555-z,x,-y1
Buried area28320 Å2
ΔGint-179.8 kcal/mol
Surface area65160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.640, 99.640, 99.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232
Components on special symmetry positions
IDModelComponents
11A-2016-

HOH

21A-2026-

HOH

31A-2027-

HOH

41A-2041-

HOH

51A-2081-

HOH

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Components

#1: Protein 3-DEHYDROQUINATE DEHYDRATASE / 3-DEHYDROQUINASE


Mass: 18499.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q48255, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-JPS / (4R,6R,7S)-2-(2-CYCLOPROPYLETHYL)-4,6,7-TRIHYDROXY-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-4-CARBOXYLIC ACID


Mass: 298.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.2
Details: 50 MM TRIS-HCL PH 7.5 1 MM 2-MERCAPTOETHANOL 1 MM ETHYLENEDIAMINETETRAACETIC ACID 200 MM SODIUM CHLORIDE 12.5 MM (4R, 6R, 7S)- 2-(2-CYCLOPROPYL)ETHYL-4,6,7-TRIHYDROXY-4,5,6, 7- ...Details: 50 MM TRIS-HCL PH 7.5 1 MM 2-MERCAPTOETHANOL 1 MM ETHYLENEDIAMINETETRAACETIC ACID 200 MM SODIUM CHLORIDE 12.5 MM (4R, 6R, 7S)- 2-(2-CYCLOPROPYL)ETHYL-4,6,7-TRIHYDROXY-4,5,6, 7-TETRAHYDROBENZO[B]THIOPHENE-4-CARBOXYLIC ACID 32% (W/V) POLYETHYLENEGLYCOL 4000 100 M SODIUM CITRATE PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 7, 2009
RadiationMonochromator: SINGLE SILICON (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 14986 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 38.9 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.9
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 39.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C4V

2c4v


Resolution: 1.85→15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.364 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WERE REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.20981 770 5.2 %RANDOM
Rwork0.18032 ---
obs0.18187 14163 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.598 Å2
Refinement stepCycle: LAST / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1153 0 20 110 1283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221239
X-RAY DIFFRACTIONr_bond_other_d0.0010.02833
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9811675
X-RAY DIFFRACTIONr_angle_other_deg0.8863.0022037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7845149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75925.6958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99415233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.368155
X-RAY DIFFRACTIONr_chiral_restr0.0850.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021342
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02223
X-RAY DIFFRACTIONr_nbd_refined0.2120.2252
X-RAY DIFFRACTIONr_nbd_other0.1780.2840
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2594
X-RAY DIFFRACTIONr_nbtor_other0.0850.2601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1690.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0871.5749
X-RAY DIFFRACTIONr_mcbond_other0.2431.5309
X-RAY DIFFRACTIONr_mcangle_it1.93421217
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2393490
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6084.5455
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.949 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.219 99 -
Rwork0.205 1993 -
obs--99.95 %

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