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Open data
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Basic information
Entry | Database: PDB / ID: 2cjf | ||||||
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Title | TYPE II DEHYDROQUINASE INHIBITOR COMPLEX | ||||||
![]() | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
![]() | LYASE / DEHYDROQUINASE / SHIKIMATE PATHWAY / DEHYDROQUINATE / DRUG DESIGN / AMINO-ACID BIOSYNTHESIS / AROMATIC 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 | ![]() ![]() ![]() | ||||||
![]() | Payne, R.J. / Riboldi-Tunnicliffe, A. / Abell, A.D. / Lapthorn, A.J. / Abell, C. | ||||||
![]() | ![]() Title: Design, synthesis, and structural studies on potent biaryl inhibitors of type II dehydroquinases. Authors: Payne, R.J. / Riboldi-Tunnicliffe, A. / Kerbarh, O. / Abell, A.D. / Lapthorn, A.J. / Abell, 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 | ![]() | 394.4 KB | Display | ![]() |
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PDB format | ![]() | 319.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.6 MB | Display | ![]() |
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Full document | ![]() | 4.7 MB | Display | |
Data in XML | ![]() | 98.7 KB | Display | |
Data in CIF | ![]() | 131.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bt4S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE BIOMOLECULE CONSISTS OF A MOLECULE FORMED BY SPACEGROUP SYMMETRY EXPANSION OF THE ASYMMETRIC UNIT. COORDINATES ARE GIVEN FOR A SINGLE ASYMMETRICUNIT OF THE PROTEIN ASSEMBLY. |
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Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 16700.801 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: RATIONALLY DESIGNED BIFUNCTIONAL INHIBITOR / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1593 molecules ![](data/chem/img/RP4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-RP4 / ( #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-TRS / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Method: vapor diffusion, sitting drop Details: PROTEIN AT 6MG/ML WAS EQUILIBRATED AGAINST A SOLUTION 15% PEG 8K, 0.1M HEPES BUFFER PH 7.5 USING THE SITING DROP METHOD. |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 20, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939283 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→65 Å / Num. obs: 1334888 / % possible obs: 90.6 % / Redundancy: 1.88 % / Biso Wilson estimate: 25.21 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 1.82 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.3 / % possible all: 78.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BT4 Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.827 / SU B: 6.641 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE G CHAIN ELECTRON DENSITY IS OF SIGNIFICANTLY POORER QUALITY WHICH IN PART EXPLAINS THE HIGH R -FACTOR AND THE PRESENCE OF ONLY 8 DODECAMERS IN THE ASU AS APPOSED TO 16 IN THE MORE ORDERED 2BT4
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→25 Å
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Refine LS restraints |
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