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- PDB-1v4i: Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyper... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v4i | ||||||
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Title | Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyperthermophilic Thermotoga maritima F132A mutant | ||||||
![]() | octoprenyl-diphosphate synthase | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Guo, R.T. / Kuo, C.J. / Chou, C.C. / Ko, T.P. / Shr, H.L. / Liang, P.H. / Wang, A.H.-J. | ||||||
![]() | ![]() 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. #1: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.6 KB | Display | ![]() |
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PDB format | ![]() | 57.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1v4eSC ![]() 1v4hC ![]() 1v4jC ![]() 1v4kC 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 33824.242 Da / Num. of mol.: 1 / Mutation: F132A 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: 2.6 Å3/Da / Density % sol: 52.35 % | |||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Na+Hepes, lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→50 Å / Num. all: 15196 / Num. obs: 14500 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 8.57 % / Biso Wilson estimate: 49.6 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 40.02 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.55 / Num. unique all: 1220 / % possible all: 81.7 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. measured all: 124260 |
Reflection shell | *PLUS % possible obs: 81.7 % |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1V4E Resolution: 2.4→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 2
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Displacement parameters | Biso mean: 49.6 Å2 | ||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.32 Å / Luzzati sigma a obs: 0.33 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree: 0.2828 / Rfactor Rwork: 0.2713 | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 0.9 |