+
Open data
-
Basic information
Entry | Database: PDB / ID: 4mc0 | ||||||
---|---|---|---|---|---|---|---|
Title | Hedycaryol apo | ||||||
![]() | Putative sesquiterpene cyclase | ||||||
![]() | LYASE / cyclase / terpenoid / Terpene alpha domain class I / helix break / helix dipol | ||||||
Function / homology | ![]() (2Z,6E)-hedycaryol synthase / terpene synthase activity / terpenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Baer, P. / Rabe, P. / Cirton, C. / Oliveira Mann, C. / Kaufmann, N. / Groll, M. / Dickschat, J. | ||||||
![]() | ![]() Title: Hedycaryol synthase in complex with nerolidol reveals terpene cyclase mechanism. Authors: Baer, P. / Rabe, P. / Citron, C.A. / de Oliveira Mann, C.C. / Kaufmann, N. / Groll, M. / Dickschat, J.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 243.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 199.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 467.8 KB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 34.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38701.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054 Gene: KSE_00200t, KSE_76540t / Plasmid: pET28c / Production host: ![]() ![]() References: UniProt: E4MYY0, Lyases; Carbon-oxygen lyases; Acting on phosphates #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.95 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M TRIS, 1.6 M (NH4)2SO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 5, 2013 |
Radiation | Monochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 25308 / Num. obs: 24119 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.5 / % possible all: 97.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: HcS Nerolidol complex Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 26.638 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.583 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.768 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|