[English] 日本語
![](img/lk-miru.gif)
- PDB-3fpl: Chimera of alcohol dehydrogenase by exchange of the cofactor bind... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3fpl | ||||||
---|---|---|---|---|---|---|---|
Title | Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of C. beijerinckii ADH by T. brockii ADH | ||||||
![]() | NADP-dependent alcohol dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / oxydoreductase / bacterial alcohol dehydrogenase / domain exchange / chimera / Metal-binding / NADP | ||||||
Function / homology | ![]() isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Felix, F. / Goihberg, E. / Shimon, L. / Burstein, Y. | ||||||
![]() | ![]() Title: Biochemical and structural properties of chimeras constructed by exchange of cofactor-binding domains in alcohol dehydrogenases from thermophilic and mesophilic microorganisms Authors: Goihberg, E. / Peretz, M. / Tel-Or, S. / Dym, O. / Shimon, L. / Frolow, F. / Burstein, Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 91.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 67.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 459.2 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fpcC ![]() 3fsrC ![]() 3ftnC ![]() 1pedS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37646.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues 153-295 inserted from alcohol dehydrogenase of ENTAMOEBA HISTOLOTICA Source: (gene. exp.) ![]() ![]() ![]() Gene: ADH1, ADH1 / Plasmid: BS-P58 / Production host: ![]() ![]() References: UniProt: P25984, UniProt: P14941, alcohol dehydrogenase (NADP+) |
---|
-Non-polymers , 6 types, 418 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-CAC / | #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.8 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 5.6 Details: Single crystals of apo-22(CTC) were obtained by the microbatch method under oil at 18 C, using the IMPAX 1-5 robot. The apo-22(CTC) (10mg/mL) was crystallized in a mixture containing 100mM ...Details: Single crystals of apo-22(CTC) were obtained by the microbatch method under oil at 18 C, using the IMPAX 1-5 robot. The apo-22(CTC) (10mg/mL) was crystallized in a mixture containing 100mM ammonium acetate, 15% (w/v) PEG 4000, 25mM NaCl, 50mM DTT, 25mM ZnCl2 and 50mM tri-citrate dihydrate (pH sodium 5.6), Microbatch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→91.67 Å / Num. obs: 28452 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 12 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2004 / % possible all: 99.8 |
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 0.41 / Cor.coef. Fo:Fc: 0.536
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PED Resolution: 1.9→19.98 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.178 / WRfactor Rwork: 0.128 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.922 / SU B: 4.521 / SU ML: 0.072 / SU R Cruickshank DPI: 0.111 / SU Rfree: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.83 Å2 / Biso mean: 24.753 Å2 / Biso min: 10.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
|