[English] 日本語
![](img/lk-miru.gif)
- PDB-5dw7: Crystal structure of the unliganded geosmin synthase N-terminal d... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5dw7 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the unliganded geosmin synthase N-terminal domain from Streptomyces coelicolor | |||||||||
![]() | Germacradienol/geosmin synthase | |||||||||
![]() | LYASE / terpene cyclase | |||||||||
Function / homology | ![]() geosmin synthase / germacradienol synthase / (-)-germacrene D synthase / germacradienol synthase activity / germacrene-D synthase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lombardi, P.M. / Harris, G.G. / Pemberton, T.A. / Matsui, T. / Weiss, T.M. / Cole, K.E. / Koksal, M. / Murphy, F.V. / Vedula, L.S. / Chou, W.K. ...Lombardi, P.M. / Harris, G.G. / Pemberton, T.A. / Matsui, T. / Weiss, T.M. / Cole, K.E. / Koksal, M. / Murphy, F.V. / Vedula, L.S. / Chou, W.K. / Cane, D.E. / Christianson, D.W. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with alpha alpha Domain Architecture That Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence. Authors: Harris, G.G. / Lombardi, P.M. / Pemberton, T.A. / Matsui, T. / Weiss, T.M. / Cole, K.E. / Koksal, M. / Murphy, F.V. / Vedula, L.S. / Chou, W.K. / Cane, D.E. / Christianson, D.W. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 73.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 52.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 423.3 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dz2C ![]() 1ps1S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 40954.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-471 / A3(2) / M145 / Gene: cyc2, SCO6073, SC9B1.20 / Plasmid: pET-21d / Production host: ![]() ![]() References: UniProt: Q9X839, germacradienol synthase, (-)-germacrene D synthase, geosmin synthase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.56 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.1 M Tris, pH 8.2, 0.5 M magnesium chloride, 28% PEG400 PH range: 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2008 |
Radiation | Monochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.202→34.34 Å / Num. all: 6883 / Num. obs: 6127 / % possible obs: 89.13 % / Redundancy: 3.7 % / Biso Wilson estimate: 54.18 Å2 / Rmerge(I) obs: 0.201 / Net I/σ(I): 6.99 |
Reflection shell | Resolution: 3.202→3.316 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4 / % possible all: 78.52 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1PS1 Resolution: 3.202→34.337 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 27.34 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.202→34.337 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|