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- PDB-2wks: Structure of Helicobacter pylori Type II Dehydroquinase with a ne... -

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Basic information

Entry
Database: PDB / ID: 2wks
TitleStructure of Helicobacter pylori Type II Dehydroquinase with a new carbasugar-thiophene inhibitor.
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / AROMATIC AMINO ACID BIOSYNTHESIS / SHIKIMIC ACID PATHWAY / 3-DEHYDROQUINATE DEHYDRATASE
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-CB6 / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsOtero, J.M. / Guardado-Calvo, P. / Llamas-Saiz, A.L. / Prazeres, V.F.V. / Tizon, L. / Castedo, L. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J.
Citation
Journal: J. Med. Chem. / Year: 2010
Title: Synthesis and biological evaluation of new nanomolar competitive inhibitors of Helicobacter pylori type II dehydroquinase. Structural details of the role of the aromatic moieties with essential residues.
Authors: Prazeres, V.F. / Tizon, L. / Otero, J.M. / Guardado-Calvo, P. / Llamas-Saiz, A.L. / van Raaij, M.J. / Castedo, L. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C.
#1: Journal: Med.Res.Rev. / Year: 2007
Title: Progress in Type II Dehydroquinase Inhibitors: From Concept to Practice.
Authors: Gonzalez-Bello, C. / Castedo, L.
#2: Journal: Chemmedchem / Year: 2008
Title: Competitive Inhibitors of Helicobacter Pylori Type II Dehydroquinase: Synthesis, Biological Evaluation, and NMR Studies.
Authors: Prazeres, V.F.V. / Sanchez-Sixto, C. / Castedo, L. / Shuh, S.W. / Lamb, H. / Hawkins, A.R. / Canada, F.J. / Jimenez-Barbero, J. / Gonzalez-Bello, C.
History
DepositionJun 17, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 / _citation_author.name
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 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_ncs_dom_lim / 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_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 / _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
D: 3-DEHYDROQUINATE DEHYDRATASE
E: 3-DEHYDROQUINATE DEHYDRATASE
F: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,09812
Polymers110,9956
Non-polymers2,1026
Water37821
1
A: 3-DEHYDROQUINATE DEHYDRATASE
B: 3-DEHYDROQUINATE DEHYDRATASE
C: 3-DEHYDROQUINATE DEHYDRATASE
D: 3-DEHYDROQUINATE DEHYDRATASE
E: 3-DEHYDROQUINATE DEHYDRATASE
F: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules

A: 3-DEHYDROQUINATE DEHYDRATASE
B: 3-DEHYDROQUINATE DEHYDRATASE
C: 3-DEHYDROQUINATE DEHYDRATASE
D: 3-DEHYDROQUINATE DEHYDRATASE
E: 3-DEHYDROQUINATE DEHYDRATASE
F: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,19624
Polymers221,99112
Non-polymers4,20512
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area27680 Å2
ΔGint-207.2 kcal/mol
Surface area68070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.850, 157.850, 99.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

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


Mass: 18499.246 Da / Num. of mol.: 6
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-CB6 / (1R,4S,5R)-1,4,5-trihydroxy-3-[(5-methyl-1-benzothiophen-2-yl)methoxy]cyclohex-2-ene-1-carboxylic acid


Mass: 350.386 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H18O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growpH: 5
Details: 26% (W/V) POLYETHYLENEGLYCOL 4000, 0.1 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID-SODIUM HYDROXIDE PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 14, 2008 / Details: BENT, VERTICALLY FOCUSSING MIRROR
RadiationMonochromator: GE(111) TRIANGULAR BENT COMPRESSING 7O FANKUCHEN CUT
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 2.95→31 Å / Num. obs: 25927 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 74.9 Å2 / Rmerge(I) obs: 0.1
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.39 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C4V

2c4v


Resolution: 2.95→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 16.444 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23555 1198 4.6 %RANDOM
Rwork0.206 ---
obs0.20742 24653 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.234 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7092 0 144 21 7257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227368
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9829954
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.06725.636330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.137151296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.9721524
X-RAY DIFFRACTIONr_chiral_restr0.0920.21110
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215520
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9351.54524
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73227266
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.65432844
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.034.52688
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 1182 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.040.05
3Ctight positional0.040.05
4Dtight positional0.040.05
5Etight positional0.040.05
6Ftight positional0.040.05
1Atight thermal0.060.5
2Btight thermal0.060.5
3Ctight thermal0.080.5
4Dtight thermal0.070.5
5Etight thermal0.070.5
6Ftight thermal0.070.5
LS refinement shellResolution: 2.95→3.106 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.307 155 -
Rwork0.293 3579 -
obs--100 %

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