[English] 日本語
![](img/lk-miru.gif)
- PDB-6k52: Hyperthermophilic GH6 cellobiohydrolase (HmCel6A) from the microb... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6k52 | ||||||
---|---|---|---|---|---|---|---|
Title | Hyperthermophilic GH6 cellobiohydrolase (HmCel6A) from the microbial flora of a Japanese hot spring | ||||||
![]() | GH6 cellobiohydrolase, HMCEL6A | ||||||
![]() | HYDROLASE / glycoside hydrolase / GH6 / thermostable | ||||||
Function / homology | 1, 4-beta cellobiohydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / ACETATE ION![]() | ||||||
Biological species | metagenome (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Baba, S. / Takeda, M. / Okuma, J. / Hirose, Y. / Nishimura, A. / Takata, M. / Oda, K. / Shibata, D. / Kondo, Y. / Kumasaka, T. | ||||||
![]() | ![]() Title: A hyperthermophilic cellobiohydrolase mined from a hot spring metagenomic data Authors: Takeda, M. / Baba, S. / Okuma, J. / Hirose, Y. / Nishimura, A. / Takata, M. / Oda, K. / Shibata, D. / Kondo, Y. / Kumasaka, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 131.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 86.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 36 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6k55C ![]() 1oc5S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 46898.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: ![]() ![]() References: cellulose 1,4-beta-cellobiosidase (non-reducing end) | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | Sequence details | FIRST MET IS A INITIATING METHIONINE. THIS DNA SEQUENCE HAS BEEN DEPOSITED TO DDBJ WITH A ...FIRST MET IS A INITIATING | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.56 Å3/Da / Density % sol: 73.05 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% (W/V) PEG 1000, 0.2M CAICIUM ACETATE, 0.1M IMIDAZOLE (PH 8.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2012 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. obs: 97033 / % possible obs: 100 % / Redundancy: 16.3 % / Biso Wilson estimate: 17.3900593193 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.018 / Rrim(I) all: 0.074 / Net I/σ(I): 36.7 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 9626 / CC1/2: 0.961 / Rpim(I) all: 0.155 / Rrim(I) all: 0.617 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1OC5 Resolution: 1.68000139531→32.9103974351 Å / SU ML: 0.176042297081 / Cross valid method: FREE R-VALUE / σ(F): 1.33476296841 / Phase error: 21.1813420271
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3657637173 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68000139531→32.9103974351 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|