[English] 日本語
![](img/lk-miru.gif)
- PDB-1v4k: Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyper... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1v4k | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyperthermophilic Thermotoga maritima S77F mutant | ||||||
![]() | octoprenyl-diphosphate synthase | ||||||
![]() | TRANSFERASE / trans-type prenyltransferase / thermophilic | ||||||
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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 76.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 57.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 447.7 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1v4eSC ![]() 1v4hC ![]() 1v4iC ![]() 1v4jC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||
2 | ![]()
| x 8|||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 33960.434 Da / Num. of mol.: 1 / Mutation: S77F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.24 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. all: 14277 / Num. obs: 13817 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 8.94 % / Biso Wilson estimate: 43.43 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 35.9 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.9 / % possible all: 82 |
Reflection | *PLUS Num. measured all: 123482 |
Reflection shell | *PLUS % possible obs: 82 % / Mean I/σ(I) obs: 2.9 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1V4E Resolution: 2.45→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 2
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.43 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati sigma a obs: 0.28 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.45→2.54 Å / Rfactor Rfree: 0.2989 / Rfactor Rwork: 0.2316 |