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Yorodumi- PDB-5xk9: Crystal structure of Isosesquilavandulyl Diphosphate Synthase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xk9 | ||||||
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Title | Crystal structure of Isosesquilavandulyl Diphosphate Synthase from Streptomyces sp. strain CNH-189 in complex with GSPP and DMAPP | ||||||
Components | Undecaprenyl diphosphate synthase | ||||||
Keywords | TRANSFERASE / prenyltransferase / antibiotic biosynthesis | ||||||
Function / homology | Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / transferase activity, transferring alkyl or aryl (other than methyl) groups / DIMETHYLALLYL DIPHOSPHATE / GERANYL S-THIOLODIPHOSPHATE / Undecaprenyl diphosphate synthase Function and homology information | ||||||
Biological species | Streptomyces sp. CNH189 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.137 Å | ||||||
Authors | Ko, T.P. / Guo, R.T. / Liu, W. / Chen, C.C. / Gao, J. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018 Title: "Head-to-Middle" and "Head-to-Tail" cis-Prenyl Transferases: Structure of Isosesquilavandulyl Diphosphate Synthase. Authors: Gao, J. / Ko, T.P. / Chen, L. / Malwal, S.R. / Zhang, J. / Hu, X. / Qu, F. / Liu, W. / Huang, J.W. / Cheng, Y.S. / Chen, C.C. / Yang, Y. / Zhang, Y. / Oldfield, E. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xk9.cif.gz | 719 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xk9.ent.gz | 596.6 KB | Display | PDB format |
PDBx/mmJSON format | 5xk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/5xk9 ftp://data.pdbj.org/pub/pdb/validation_reports/xk/5xk9 | HTTPS FTP |
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-Related structure data
Related structure data | 5xk3SC 5xk6C 5xk7C 5xk8C 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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Unit cell |
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-Components
#1: Protein | Mass: 26708.215 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. CNH189 (bacteria) / Gene: mcl22 / Plasmid: pET46Ek/LIC Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: M4T4U9 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GST / #4: Chemical | ChemComp-DMA / #5: 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: 2.52 Å3/Da / Density % sol: 51.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: PROTEIN: 10 mg/mL in a buffer containing 25 mM Tris-Cl (pH 7.5), 150 mM NaCl RESERVOIR: 0.2 M Na citrate, 20% v/v polyethylene glycol (PEG) 3350 SOAKING: 5 mM MgCl2, 50 mM Na citrate, 24% ...Details: PROTEIN: 10 mg/mL in a buffer containing 25 mM Tris-Cl (pH 7.5), 150 mM NaCl RESERVOIR: 0.2 M Na citrate, 20% v/v polyethylene glycol (PEG) 3350 SOAKING: 5 mM MgCl2, 50 mM Na citrate, 24% v/v PEG 3350, 10% v/v glycerol, 10 mM GSPP, 10 mM DMAPP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 28, 2017 |
Radiation | Monochromator: LN2 cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 2.137→25 Å / Num. obs: 115165 / % possible obs: 98.1 % / Redundancy: 3.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.14→2.21 Å / Redundancy: 3 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 11565 / CC1/2: 0.929 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XK3 Resolution: 2.137→24.78 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.137→24.78 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 30.2117 Å / Origin y: 9.1126 Å / Origin z: 12.5328 Å
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Refinement TLS group | Selection details: all |