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- PDB-1wl2: Crystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyper... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1wl2 | ||||||
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Title | Crystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyperthermophilic Thermotoga Maritima R90A mutant | ||||||
![]() | octoprenyl-diphosphate synthase | ||||||
![]() | TRANSFERASE / trans-type prenyltransferase / thermophilic | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Guo, R.T. / Kuo, C.J. / Cheng, Y.S. / Cheng, Y.L. / Liang, P.H. / Wang, A.H.-J. | ||||||
![]() | ![]() Title: Biochemical and Structural Basis for Octaprenyl Pyrophosphate Synthase Authors: Guo, R.T. / Kuo, C.J. / Cheng, Y.S. / Cheng, Y.L. / Liang, P.H. / Wang, A.H.-J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Preliminary X-ray diffraction analysis of octaprenyl pyrophosphate synthase crystals from Thermotoga maritima and Escherichia coli Authors: Guo, R.T. / Ko, T.P. / Chou, C.C. / Shr, H.L. / Chu, H.M. / Tsai, Y.H. / Liang, P.H. / Wang, A.H.-J. #2: ![]() Title: Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyperthermophilic Thermotoga maritima and Mechanism of Product Chain Length Determination Authors: Guo, R.T. / Kuo, C.J. / Chou, C.C. / Ko, T.P. / Shr, H.L. / Liang, P.H. / Wang, A.H.-J. #3: ![]() Title: A Molecular Ruler for Chain Elongation Catalyzed by Octaprenyl Pyrophosphate Synthase and Its Structure-Based Engineering to Produce Unprecedented Long-Chain Trans-Prenyl Products Authors: Guo, R.T. / Kuo, C.J. / Ko, T.P. / Chou, C.C. / Liang, P.H. / Wang, A.H.-J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.6 KB | Display | ![]() |
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PDB format | ![]() | 55.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.8 KB | Display | ![]() |
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Full document | ![]() | 445 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wkzC ![]() 1wl0C ![]() 1wl1C ![]() 1wl3C ![]() 1v4eS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 33814.223 Da / Num. of mol.: 1 / Mutation: R90A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Tris-HCl, NaCl, HEPES, Lithium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 10, 2004 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 9507 / Num. obs: 9426 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Redundancy: 7.94 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 24.92 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 3.78 / Num. unique all: 917 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1V4E Resolution: 2.8→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 46.36 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.32 Å / Luzzati sigma a obs: 0.34 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å
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