+Open data
-Basic information
Entry | Database: PDB / ID: 5gk0 | ||||||
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Title | Crystal structure of selnomethionin-labeled ketosynthase StlD | ||||||
Components | Ketosynthase StlD | ||||||
Keywords | TRANSFERASE / Ketosynthase | ||||||
Function / homology | 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / secondary metabolite biosynthetic process / acyltransferase activity / Thiolase-like / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 8/17 Function and homology information | ||||||
Biological species | Photorhabdus luminescens subsp. laumondii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.331 Å | ||||||
Authors | Mori, T. / Saito, Y. / Morita, H. / Abe, I. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2016 Title: Structural Insight into the Enzymatic Formation of Bacterial Stilbene. Authors: Mori, T. / Awakawa, T. / Shimomura, K. / Saito, Y. / Yang, D. / Morita, H. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gk0.cif.gz | 307.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gk0.ent.gz | 260.5 KB | Display | PDB format |
PDBx/mmJSON format | 5gk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gk0_validation.pdf.gz | 467.7 KB | Display | wwPDB validaton report |
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Full document | 5gk0_full_validation.pdf.gz | 488.7 KB | Display | |
Data in XML | 5gk0_validation.xml.gz | 57.2 KB | Display | |
Data in CIF | 5gk0_validation.cif.gz | 81.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/5gk0 ftp://data.pdbj.org/pub/pdb/validation_reports/gk/5gk0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45486.859 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (bacteria) Strain: DSM 15139 / CIP 105565 / TT01 / Gene: plu2164 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus / References: UniProt: Q7N4Z6 #2: 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: 2.4 Å3/Da / Density % sol: 48.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 12.5% PEG 4000, 100mM Tris-HCl (pH7.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9788 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 14, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 143308 / % possible obs: 99.3 % / Redundancy: 3.81 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.32 |
Reflection shell | Resolution: 2.33→2.47 Å / Redundancy: 3.67 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 8.03 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.331→41.73 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.331→41.73 Å
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Refine LS restraints |
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LS refinement shell |
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