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- PDB-1v4h: Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyper... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v4h | ||||||
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Title | Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyperthermophilic Thermotoga maritima F52A 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.7 KB | Display | ![]() |
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PDB format | ![]() | 56.3 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 ![]() 1v4iC ![]() 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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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: 33824.242 Da / Num. of mol.: 1 / Mutation: F52A 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: 2.66 Å3/Da / Density % sol: 53.46 % | |||||||||||||||||||||||||||||||||||
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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: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 9757 / Num. obs: 9680 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 9.27 % / Biso Wilson estimate: 52.79 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 32.87 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 4.27 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. measured all: 89703 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.45 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1V4E Resolution: 2.8→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 2
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Displacement parameters | Biso mean: 52.79 Å2 | ||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.33 Å / Luzzati sigma a obs: 0.39 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 / Rfactor Rfree: 0.3416 / Rfactor Rwork: 0.2793 | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |