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- PDB-4b6r: Structure of Helicobacter pylori Type II Dehydroquinase inhibited... -

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Basic information

Entry
Database: PDB / ID: 4b6r
TitleStructure of Helicobacter pylori Type II Dehydroquinase inhibited by (2S)-2-(4-methoxy)benzyl-3-dehydroquinic acid
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE
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-3DQ / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOtero, J.M. / Llamas-Saiz, A.L. / Lence, E. / Tizon, L. / Peon, A. / Prazeres, V.F.V. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J.
CitationJournal: ACS Chem. Biol. / Year: 2013
Title: Mechanistic basis of the inhibition of type II dehydroquinase by (2S)- and (2R)-2-benzyl-3-dehydroquinic acids.
Authors: Lence, E. / Tizon, L. / Otero, J.M. / Peon, A. / Prazeres, V.F. / Llamas-Saiz, A.L. / Fox, G.C. / van Raaij, M.J. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C.
History
DepositionAug 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other / Structure summary
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Aug 7, 2013Group: Non-polymer description
Revision 1.4Sep 17, 2014Group: Atomic model / Derived calculations / Non-polymer description
Revision 1.5Jan 17, 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 1.6Dec 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
B: 3-DEHYDROQUINATE DEHYDRATASE
C: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5257
Polymers55,4983
Non-polymers1,0274
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-48.1 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.436, 100.436, 104.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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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 26695 (bacteria) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q48255, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-3DQ / (1R,2S,4S,5R)-2-(4-methoxyphenyl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid


Mass: 310.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H18O7
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 5.4
Details: 50 MM TRIS-HCL PH 7.5, 1 MM 2-MERCAPTOETHANOL, 1 MM ETHYLENEDIAMINETETRAACETIC ACID, 200 MM SODIUM CHLORIDE 36% (W/V) POLYETHYLENEGLYCOL 4000, 0.1 M SODIUM CITRATE PH 5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2010 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2→58.7 Å / Num. obs: 36522 / % possible obs: 99.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 4.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C4V

2c4v


Resolution: 2→58.7 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.888 / SU B: 5.176 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27603 1876 5.1 %THIN SHELLS
Rwork0.21151 ---
obs0.21493 34582 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: 45.424 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2→58.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 71 179 3889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223848
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9795195
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9585469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97126.044182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61315705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2181512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212868
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2051764
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22644
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0971.52340
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91823776
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.21931508
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5644.51418
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: 2→2.108 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.33 248 -
Rwork0.27 4973 -
obs--99.9 %

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