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- PDB-2xd9: STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLE... -

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Basic information

Entry
Database: PDB / ID: 2xd9
TitleSTRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (4R,6R,7S)-4,6,7-Trihydroxy-2-((E)-prop-1- enyl)-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-XD9 / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPaz, 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.
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 / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _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

Downloads & links

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Assembly

Deposited unit
A: 3-DEHYDROQUINATE DEHYDRATASE
B: 3-DEHYDROQUINATE DEHYDRATASE
C: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3096
Polymers55,4983
Non-polymers8113
Water5,152286
1
A: 3-DEHYDROQUINATE DEHYDRATASE
B: 3-DEHYDROQUINATE DEHYDRATASE
C: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules

A: 3-DEHYDROQUINATE DEHYDRATASE
B: 3-DEHYDROQUINATE DEHYDRATASE
C: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules

A: 3-DEHYDROQUINATE DEHYDRATASE
B: 3-DEHYDROQUINATE DEHYDRATASE
C: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules

A: 3-DEHYDROQUINATE DEHYDRATASE
B: 3-DEHYDROQUINATE DEHYDRATASE
C: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,23524
Polymers221,99112
Non-polymers3,24412
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_555-x,y,-z1
Buried area28790 Å2
ΔGint-184.3 kcal/mol
Surface area67550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.217, 100.217, 103.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11B-2067-

HOH

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Components

#1: Protein 3-DEHYDROQUINATE DEHYDRATASE / 3-DEHYDROQUINASE / TYPE II DHQASE


Mass: 18499.246 Da / Num. of mol.: 3
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-XD9 / (4R,6R,7S)-4,6,7-TRIHYDROXY-2-[(1E)-PROP-1-EN-1-YL]-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-4-CARBOXYLIC ACID


Mass: 270.302 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H14O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.35 Å3/Da / Density % sol: 47.7 % / Description: NONE
Crystal growpH: 5.8
Details: 50 MM TRIS-HCL PH 7.5 1 MM 2-MERCAPTOETHANOL 1 MM ETHYLENEDIAMINETETRAACETIC ACID 200 MM SODIUM CHLORIDE 24% (W/V) POLYETHYLENEGLYCOL 4000 100 MM SODIUM CITRATE, PH 5.8 12.5 MM (4R, 6R, 7S)- ...Details: 50 MM TRIS-HCL PH 7.5 1 MM 2-MERCAPTOETHANOL 1 MM ETHYLENEDIAMINETETRAACETIC ACID 200 MM SODIUM CHLORIDE 24% (W/V) POLYETHYLENEGLYCOL 4000 100 MM SODIUM CITRATE, PH 5.8 12.5 MM (4R, 6R, 7S)-4,6, 7-TRIHYDROXY-2-[(E)-PROP-1-ENYL]-4,5,6, 7-TETRAHYDROBENZO[B]THIOPHENE-4-CARBOXYLIC ACID 0.13 % (V/V) METHANOL

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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: 1.95→34 Å / Num. obs: 38626 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.8
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.8 / % possible all: 99.7

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Processing

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

2c4v


Resolution: 1.95→15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.426 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25025 1536 4 %THIN SHELLS
Rwork0.2105 ---
obs0.21218 36894 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.237 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2---0.75 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 54 286 3868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223721
X-RAY DIFFRACTIONr_bond_other_d0.0010.022464
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.9755029
X-RAY DIFFRACTIONr_angle_other_deg0.8943.0016049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7525454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52125.886175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43315678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6721512
X-RAY DIFFRACTIONr_chiral_restr0.090.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024091
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02679
X-RAY DIFFRACTIONr_nbd_refined0.2120.2819
X-RAY DIFFRACTIONr_nbd_other0.1810.22554
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21764
X-RAY DIFFRACTIONr_nbtor_other0.0860.21789
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2266
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0170.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1440.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9731.52270
X-RAY DIFFRACTIONr_mcbond_other0.1891.5941
X-RAY DIFFRACTIONr_mcangle_it1.71723671
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.14331451
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2624.51358
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: 1.95→2.054 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.31 193 -
Rwork0.288 5302 -
obs--99.76 %

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