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- PDB-2c4w: Type II Dehydroquinase from H. pylori in complex with AH9095 -

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Basic information

Entry
Database: PDB / ID: 2c4w
TitleType II Dehydroquinase from H. pylori in complex with AH9095
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / 3-DEHYDROQUINASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / DEHYDROQUINATE / SULPHONAMIDE
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
N-TETRAZOL-5-YL 9-OXO-9H-XANTHENE-2 SULPHONAMIDE / IMIDAZOLE / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRobinson, D.A. / Lapthorn, A.J.
CitationJournal: J.Med.Chem. / Year: 2006
Title: Crystal Structures of Helicobacter Pylori Type II Dehydroquinase Inhibitor Complexes: New Directions for Inhibitor Design.
Authors: Robinson, D.A. / Stewart, K.A. / Price, N.C. / Chalk, P.A. / Coggins, J.R. / Lapthorn, A.J.
History
DepositionOct 24, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0566
Polymers19,3901
Non-polymers6665
Water2,342130
1
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules

A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,11212
Polymers38,7812
Non-polymers1,33110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation27_556-x+1/2,y,-z+3/21
MethodPQS
Unit cell
Length a, b, c (Å)131.370, 131.370, 131.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23

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Components

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


Mass: 19390.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: Q48255, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-GAJ / N-TETRAZOL-5-YL 9-OXO-9H-XANTHENE-2 SULPHONAMIDE / N-(1,4-DIHYDRO-5H-TETRAZOL-5-YLIDENE)-9-OXO-9H-XANTHENE-2-SULFONAMIDE


Mass: 343.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9N5O4S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES A TRANS-DEHYDRATION VIA AN ENOLATE INTERMEDIATE.

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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: 2.13 Å3/Da / Density % sol: 37.8 %
Crystal growpH: 8.2
Details: 10MG/ML PROTEIN CRYSTLLISED AGAINST 1.0M NA ACETATE, 0.1M IMIDAZOLE-HCL PH 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 12, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 27302 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 24
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DHQ

2dhq


Resolution: 1.55→25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.688 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2564 10 %RANDOM
Rwork0.152 ---
obs0.156 23103 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.93 Å2
Refinement stepCycle: LAST / Resolution: 1.55→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 0 46 130 1451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221482
X-RAY DIFFRACTIONr_bond_other_d0.0010.021337
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9812005
X-RAY DIFFRACTIONr_angle_other_deg0.88533114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4585192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59825.75866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37815247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.861155
X-RAY DIFFRACTIONr_chiral_restr0.0860.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021675
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02290
X-RAY DIFFRACTIONr_nbd_refined0.2350.2279
X-RAY DIFFRACTIONr_nbd_other0.1720.21178
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2639
X-RAY DIFFRACTIONr_nbtor_other0.0850.2746
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8781.51217
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.121482
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3793640
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.274.5519
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: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.229 144
Rwork0.175 1498

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