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Yorodumi- PDB-4v0s: Crystal structure of Mycobacterium tuberculosis Type II Dehydroqu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v0s | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis Type II Dehydroquinase D88N mutant inhibited by a 3-dehydroquinic acid derivative | ||||||
Components | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
Keywords | LYASE / BINDING SITES / 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: 1.55 Å | ||||||
Authors | Otero, J.M. / Llamas-Saiz, A.L. / Santiago, C. / Lamb, H. / Hawkins, A.R. / Maneiro, M. / Peon, A. / 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. / van Raaij, M.J. / Lamb, H. / Hawkings, A.R. / 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 | 4v0s.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v0s.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 4v0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v0s_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 4v0s_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4v0s_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 4v0s_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/4v0s ftp://data.pdbj.org/pub/pdb/validation_reports/v0/4v0s | HTTPS FTP |
-Related structure data
Related structure data | 4ckwC 4ckxC 4ckyC 4ckzC 4cl0C 2y71S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 15675.753 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): SK3430 References: UniProt: P9WPX6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase |
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-Non-polymers , 5 types, 157 molecules
#2: Chemical | #3: Chemical | ChemComp-7HN / | #4: Chemical | #5: Chemical | ChemComp-NA / | #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: 1.99 Å3/Da / Density % sol: 38.27 % / Description: NONE |
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Crystal grow | pH: 6.2 / Details: 28% PEG4000, 100 MM NA-CITRATE PH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.00227 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2014 / Details: PLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR) |
Radiation | Monochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00227 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→94.75 Å / Num. obs: 34076 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.9 / % possible all: 76.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y71 Resolution: 1.55→53.71 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.017 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY. GAP BY DISORDERED REGION BETWEEN ALA-107 AND HIS-114 IN CHAIN A.
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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: 19.382 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→53.71 Å
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Refine LS restraints |
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