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Open data
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Basic information
Entry | Database: PDB / ID: 2bt4 | ||||||
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Title | Type II Dehydroquinase inhibitor complex | ||||||
![]() | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
![]() | LYASE / SHIKIMATE PATHWAY / DEHYDROQUINATE / 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 | ![]() ![]() ![]() | ||||||
![]() | Toscano, M.D. / Stewart, K.A. / Coggins, J.R. / Lapthorn, A.J. / Abell, C. | ||||||
![]() | ![]() Title: Rational Design of New Bifunctional Inhibitors of Type II Dehydroquinase. Authors: Toscano, M.D. / Stewart, K.A. / Coggins, J.R. / Lapthorn, A.J. / Abell, C. #1: ![]() Title: The Structure and Mechanism of the Type II Dehydroquinase from Streptomyces Coelicolor Authors: Roszak, A.W. / Robinson, D.A. / Krell, T. / Hunter, I.S. / Frederickson, M. / Abell, C. / Coggins, J.R. / Lapthorn, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 394.7 KB | Display | ![]() |
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PDB format | ![]() | 318.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 917.6 KB | Display | ![]() |
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Full document | ![]() | 962.1 KB | Display | |
Data in XML | ![]() | 40 KB | Display | |
Data in CIF | ![]() | 68 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gu1S 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 domain:
NCS domain segments:
NCS oper:
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Details | THE BIOMOLECULE CONSISTS OF A MOLECULEFORMED BY SPACEGROUP SYMMETRY EXPANSION OF THEASYMMETRIC 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, 1763 molecules ![](data/chem/img/CA2.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA2 / ( #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-TRS / #5: Chemical | ChemComp-GOL / #6: 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: 42 % |
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Crystal grow | pH: 6.5 Details: 15% PEG8K, 0.2M NAKPHOSPHATE, 0.1M MOPS/HCL PH6.5, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 25, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 3557702 / % possible obs: 93.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 2.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GU1 Resolution: 1.7→27 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.669 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS IS A SUPERLATTICE STRUCTURE
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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: 12.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→27 Å
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