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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 | ||||||
Components | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
Keywords | LYASE / SHIKIMATE PATHWAY / DEHYDROQUINATE / AMINO-ACID BIOSYNTHESIS / AROMATIC AMINO ACID BIOSYNTHESIS | ||||||
| Function / homology | Function and homology informationquinate 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 | STREPTOMYCES COELICOLOR (bacteria) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Toscano, M.D. / Stewart, K.A. / Coggins, J.R. / Lapthorn, A.J. / Abell, C. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2005Title: 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: Journal: Structure / Year: 2002Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2bt4.cif.gz | 394.7 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2bt4.ent.gz | 318.4 KB | Display | PDB format |
| PDBx/mmJSON format | 2bt4.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 2bt4_validation.pdf.gz | 917.6 KB | Display | wwPDB validaton report |
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| Full document | 2bt4_full_validation.pdf.gz | 962.1 KB | Display | |
| Data in XML | 2bt4_validation.xml.gz | 40 KB | Display | |
| Data in CIF | 2bt4_validation.cif.gz | 68 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/2bt4 ftp://data.pdbj.org/pub/pdb/validation_reports/bt/2bt4 | 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.) STREPTOMYCES COELICOLOR (bacteria) / Plasmid: PDHQ / Production host: ![]() |
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-Non-polymers , 5 types, 1763 molecules 








| #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
| 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: MOLECULAR REPLACEMENTStarting 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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| Refine LS restraints |
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About Yorodumi




STREPTOMYCES COELICOLOR (bacteria)
X-RAY DIFFRACTION
Citation












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