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Yorodumi- PDB-2cb9: Crystal structure of the thioesterase domain of the fengycin bios... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cb9 | ||||||
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Title | Crystal structure of the thioesterase domain of the fengycin biosynthesis cluster | ||||||
Components | FENGYCIN SYNTHETASE | ||||||
Keywords | HYDROLASE / THIOESTERASE / NON-RIBOSOMAL PEPTIDE SYNTHESIS / ALPHA/BETA-HYDROLASES / CATALYTIC TRIADE | ||||||
Function / homology | Function and homology information amino acid activation for nonribosomal peptide biosynthetic process / carboxylic acid metabolic process / secondary metabolite biosynthetic process / phosphopantetheine binding / antibiotic biosynthetic process / catalytic activity / cytosol Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Samel, S. / Marahiel, M.A. / Essen, L.-O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: The Thioesterase Domain of the Fengycin Biosynthesis Cluster: A Structural Base for the Macrocyclization of a Non-Ribosomal Lipopeptide Authors: Samel, S. / Wagner, B. / Marahiel, M.A. / Essen, L.-O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cb9.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cb9.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 2cb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cb9_validation.pdf.gz | 443.8 KB | Display | wwPDB validaton report |
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Full document | 2cb9_full_validation.pdf.gz | 446.4 KB | Display | |
Data in XML | 2cb9_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 2cb9_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/2cb9 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/2cb9 | HTTPS FTP |
-Related structure data
Related structure data | 2cbgC 1jmkS 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
#1: Protein | Mass: 27522.734 Da / Num. of mol.: 1 / Fragment: THIOESTERASE DOMAIN RESIDUES 1043-1274 Source method: isolated from a genetically manipulated source Details: RECOMBINANT FRAGMENT OF THE NRPS SYNTHETASE FENB (Q1043-H1274) Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: F29-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / Variant (production host): PREP4 / References: UniProt: Q45563 |
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#2: Chemical | ChemComp-ACY / |
#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: 2.6 Å3/Da / Density % sol: 53 % |
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Crystal grow | pH: 5.6 Details: 0.2 M NH4 ACETATE; 0.1 M NA CITRATE (PH 5.6); 22.5 % PEG 8000, 10 MG/ML PROTEIN |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 2003 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→24 Å / Num. obs: 26374 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / % possible all: 93.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JMK Resolution: 1.8→24.35 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.862 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES T123-S129 WERE DISORDERED AND OMITTED FROM THE STRUCTURAL MODEL
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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: 17.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→24.35 Å
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Refine LS restraints |
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