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- PDB-2xb9: Structure of Helicobacter pylori type II dehydroquinase in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xb9 | ||||||
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Title | Structure of Helicobacter pylori type II dehydroquinase in complex with inhibitor compound (2R)-2-(4-methoxybenzyl)-3-dehydroquinic acid | ||||||
![]() | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
![]() | LYASE / AMINO ACID BIOSYNTHESIS | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Otero, J.M. / Tizon, L. / Llamas-Saiz, A.L. / Fox, G.C. / Gonzalez-Bello, C. / van Raaij, M.J. | ||||||
![]() | ![]() Title: Understanding the Key Factors that Control the Inhibition of Type II Dehydroquinase by (2R)-2- Benzyl-3-Dehydroquinic Acids. Authors: Peon, A. / Otero, J.M. / Tizon, L. / Prazeres, V.F.V. / Llamas-Saiz, A.L. / Fox, G.C. / van Raaij, M.J. / Lamb, H. / Hawkins, A.R. / Gago, F. / Castedo, L. / Gonzalez-Bello, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.5 KB | Display | ![]() |
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PDB format | ![]() | 81 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1008.6 KB | Display | ![]() |
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Full document | ![]() | 1016.9 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xb8C ![]() 2c4vS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 18499.246 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CIT / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 5 Details: 20 MG/ML DEHYDROQUINASE; 12.5 MM 2R)-2-(4-METHOXYBENZYL)-3-DEHYDROQUINIC ACID, 50 MM TRIS-HCL PH 7.5, 1 MM 2-MERCAPTOETHANOL, 1 MM ETHYLENEDIAMINETETRAACETIC ACID, 200 MM SODIUM CHLORIDE; ...Details: 20 MG/ML DEHYDROQUINASE; 12.5 MM 2R)-2-(4-METHOXYBENZYL)-3-DEHYDROQUINIC ACID, 50 MM TRIS-HCL PH 7.5, 1 MM 2-MERCAPTOETHANOL, 1 MM ETHYLENEDIAMINETETRAACETIC ACID, 200 MM SODIUM CHLORIDE; 31% (W/V) POLYETHYLENEGLYCOL 4000, 0.1 M SODIUM CITRATE PH 5.0 |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS KAPPA CCD-2000 / Detector: CCD / Date: Oct 5, 2009 / Details: CONFOCAL MULTILAYER GRADED MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→35 Å / Num. obs: 14629 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 61.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.68 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.39 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2C4V Resolution: 2.75→34.22 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.903 / SU B: 13.843 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.463 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→34.22 Å
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Refine LS restraints |
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