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Yorodumi- PDB-4b6p: Structure of Mycobacterium tuberculosis Type II Dehydroquinase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b6p | ||||||
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Title | Structure of Mycobacterium tuberculosis Type II Dehydroquinase inhibited by (2S)-2-Perfluorobenzyl-3-dehydroquinic acid | ||||||
Components | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information quinate catabolic process / Chorismate via Shikimate Pathway / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Otero, J.M. / Llamas-Saiz, A.L. / Lence, E. / Tizon, L. / Peon, A. / Prazeres, V.F.V. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2013 Title: Mechanistic basis of the inhibition of type II dehydroquinase by (2S)- and (2R)-2-benzyl-3-dehydroquinic acids. Authors: Lence, E. / Tizon, L. / Otero, J.M. / Peon, A. / Prazeres, V.F. / Llamas-Saiz, A.L. / Fox, G.C. / van Raaij, M.J. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b6p.cif.gz | 44.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b6p.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 4b6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b6p_validation.pdf.gz | 820.8 KB | Display | wwPDB validaton report |
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Full document | 4b6p_full_validation.pdf.gz | 822.4 KB | Display | |
Data in XML | 4b6p_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 4b6p_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/4b6p ftp://data.pdbj.org/pub/pdb/validation_reports/b6/4b6p | HTTPS FTP |
-Related structure data
Related structure data | 4b6oC 4b6qC 4b6rC 4b6sC 1h0sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15676.737 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): SK3430 References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase | ||||
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#2: Chemical | ChemComp-2HN / ( | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | INITIATOR METHIONINE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 50 MM TRIS-HCL PH 7.5 1 MM 2-MERCAPTOETHANOL 1 MM ETHYLENEDIAMINETETRAACETIC ACID 200 MM SODIUM CHLORIDE 20% (W/V) POLYETHYLENEGLYCOL 2000ME 0.1 M 3-(N-MORPHOLINO)PROPANESULFONIC ACID (MOPS) PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2010 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS |
Radiation | Monochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→44.64 Å / Num. obs: 7534 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.3→2.43 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H0S Resolution: 2.3→44.64 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.086 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.214 / 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: 15.884 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→44.64 Å
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Refine LS restraints |
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