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Yorodumi- PDB-3wjk: Crystal structure of Octaprenyl Pyrophosphate synthase from Esche... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wjk | ||||||
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Title | Crystal structure of Octaprenyl Pyrophosphate synthase from Escherichia coli | ||||||
Components | Octaprenyl diphosphate synthase | ||||||
Keywords | TRANSFERASE / prenyltransferase / site-directed mutagenesis / product chain length | ||||||
Function / homology | Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Orthogonal Bundle / Mainly Alpha / : Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Han, X. / Chen, C.C. / Kuo, C.J. / Huang, C.H. / Zheng, Y. / Ko, T.P. / Zhu, Z. / Feng, X. / Oldfield, E. / Liang, P.H. ...Han, X. / Chen, C.C. / Kuo, C.J. / Huang, C.H. / Zheng, Y. / Ko, T.P. / Zhu, Z. / Feng, X. / Oldfield, E. / Liang, P.H. / Guo, R.T. / Ma, Y.H. | ||||||
Citation | Journal: Proteins / Year: 2015 Title: Crystal structures of ligand-bound octaprenyl pyrophosphate synthase from Escherichia coli reveal the catalytic and chain-length determining mechanisms. Authors: Han, X. / Chen, C.C. / Kuo, C.J. / Huang, C.H. / Zheng, Y. / Ko, T.P. / Zhu, Z. / Feng, X. / Wang, K. / Oldfield, E. / Wang, A.H. / Liang, P.H. / Guo, R.T. / Ma, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wjk.cif.gz | 133.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wjk.ent.gz | 103.2 KB | Display | PDB format |
PDBx/mmJSON format | 3wjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/3wjk ftp://data.pdbj.org/pub/pdb/validation_reports/wj/3wjk | HTTPS FTP |
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-Related structure data
Related structure data | 3wjnC 3wjoC 3mzvS 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: 36969.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O104:H4 str. 2009EL-2071 / Gene: O3O_22640 / Plasmid: pET46a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: K0BUH0, Transferases; Transferring alkyl or aryl groups, other than methyl groups #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: 2.35 Å3/Da / Density % sol: 47.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.3M Magnesium chloride hexahydrate, 0.1M Tris-HCl pH 8.5, 24% w/v polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 36336 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 3 / Num. unique all: 13763 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MZV Resolution: 2.2→25 Å / Occupancy max: 1 / Occupancy min: 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 39.727 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 90.28 Å2 / Biso mean: 45.9341 Å2 / Biso min: 16.11 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å /
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