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Yorodumi- PDB-4c6x: Crystal structure of M. tuberculosis C171Q KasA in complex with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c6x | ||||||
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Title | Crystal structure of M. tuberculosis C171Q KasA in complex with thiolactomycin (TLM) | ||||||
Components | 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1 | ||||||
Keywords | TRANSFERASE / KASA / KAS ENZYME / CONDENSING ENZYME / TYPE 2 FATTY ACID BIOSYNTHESIS / MYCOLIC ACID SYNTHESIS | ||||||
Function / homology | Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / : / Chem-M7U / THIOLACTOMYCIN / : Function and homology information | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS H37RV (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Schiebel, J. / Kapilashrami, K. / Fekete, A. / Bommineni, G.R. / Schaefer, C.M. / Mueller, M.J. / Tonge, P.J. / Kisker, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural Basis for the Recognition of Mycolic Acid Precursors by Kasa, a Condensing Enzyme and Drug Target from Mycobacterium Tuberculosis Authors: Schiebel, J. / Kapilashrami, K. / Fekete, A. / Bommineni, G.R. / Schaefer, C.M. / Mueller, M.J. / Tonge, P.J. / Kisker, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c6x.cif.gz | 337.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c6x.ent.gz | 274 KB | Display | PDB format |
PDBx/mmJSON format | 4c6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/4c6x ftp://data.pdbj.org/pub/pdb/validation_reports/c6/4c6x | HTTPS FTP |
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-Related structure data
Related structure data | 4c6uC 4c6vC 4c6wC 4c6zC 4c70C 4c71C 4c72C 4c73C 2wggS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45845.676 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS H37RV (bacteria) Plasmid: PFPCA1 / Production host: MYCOBACTERIUM SMEGMATIS (bacteria) / Strain (production host): MC2155 References: UniProt: I6Y8T4, beta-ketoacyl-[acyl-carrier-protein] synthase I |
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-Non-polymers , 6 types, 768 molecules
#2: Chemical | ChemComp-EDO / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EPE / | #7: 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: 3.5 Å3/Da / Density % sol: 64.91 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1 M HEPES PH 7.5, 30% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.45 Å / Num. obs: 87684 / % possible obs: 98.3 % / Observed criterion σ(I): 6 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.7 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WGG Resolution: 1.95→91.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.016 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.803 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→91.5 Å
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Refine LS restraints |
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