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Yorodumi- PDB-4cl0: Structure of the Mycobacterium tuberculosis Type II Dehydroquinas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cl0 | ||||||
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Title | Structure of the Mycobacterium tuberculosis Type II Dehydroquinase inhibited by a 3-dehydroquinic acid derivative | ||||||
Components | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
Keywords | LYASE / BACTERIAL PROTEINS / TYPE 2 DEHYDROQUINASE / INHIBITOR / PROTEIN BINDING / SHIKIMIS ACID PATHWAY / SUBSTRATE SPECIFICITY | ||||||
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: 3.1 Å | ||||||
Authors | Otero, J.M. / Llamas-Saiz, A.L. / Maneiro, M. / Peon, A. / Sedes, A. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J. | ||||||
Citation | Journal: To be Published Title: Investigation of the Dehydratation Mechanism Catalyzed by the Type II Dehydroquinase Authors: Maneiro, M. / Otero, J.M. / Peon, A. / Sedes, A. / Llamas-Saiz, A.L. / Lamb, H. / Hawkins, A.R. / van Raaij, M.J. / Gonzalez-Bello, C. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cl0.cif.gz | 40.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cl0.ent.gz | 28.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cl0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/4cl0 ftp://data.pdbj.org/pub/pdb/validation_reports/cl/4cl0 | HTTPS FTP |
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-Related structure data
Related structure data | 4ckwC 4ckxC 4ckyC 4ckzC 4v0sC 2y71S C: citing same article (ref.) S: Starting model for refinement |
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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): BL21 / Variant (production host): SK3430 References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase |
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#2: Chemical | ChemComp-9PY / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.7 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 32% (V/V) 2-METHYL-2,4-PENTANEDIOL, 0.3 M AMMONIUM SULFATE, 0.1 M 4-(2-HYDROXYETHYL)-PIPERAZINE- 1-ETHANESULFONIC ACID SODIUM SALT (HEPES) PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97908 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2013 / Details: CYLINDRICAL GRAZING INCIDENCE MIRROR |
Radiation | Monochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→44.55 Å / Num. obs: 3177 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 7.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y71 Resolution: 3.1→44.59 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.862 / SU B: 15.61 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY. ARG-18 AND GLU-42 SIDE CHAINS ARE MISSING BY DISORDER IN THE STRUCTURE. INHIBITOR INCLUDED IN ENZYME ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY. ARG-18 AND GLU-42 SIDE CHAINS ARE MISSING BY DISORDER IN THE STRUCTURE. INHIBITOR INCLUDED IN ENZYME ACTIVE SITE BY SOAKING OF APO-CRYSTALS IN INHIBITOR SOLUTION
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.75 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→44.59 Å
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Refine LS restraints |
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