[English] 日本語
![](img/lk-miru.gif)
- PDB-1kbj: Crystallographic Study of the Recombinant Flavin-binding Domain o... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1kbj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast Flavocytochrome b2: comparison with the Intact Wild-type Enzyme | ||||||
![]() | CYTOCHROME B2 | ||||||
![]() | OXIDOREDUCTASE / flavin-binding domain of flavocytochrome b2 | ||||||
Function / homology | ![]() L-lactate dehydrogenase (cytochrome) / L-lactate dehydrogenase (cytochrome) activity / lactate metabolic process / : / mitochondrial intermembrane space / mitochondrial inner membrane / heme binding / mitochondrion / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cunane, L.M. / Barton, J.D. / Chen, Z.W. / Welsh, F.E. / Chapman, S.K. / Reid, G.A. / Mathews, F.S. | ||||||
![]() | ![]() Title: Crystallographic study of the recombinant flavin-binding domain of Baker's yeast flavocytochrome b(2): comparison with the intact wild-type enzyme. Authors: Cunane, L.M. / Barton, J.D. / Chen, Z.W. / Welsh, F.E. / Chapman, S.K. / Reid, G.A. / Mathews, F.S. #1: ![]() Title: Molecular Structure of Flavocytochrome b2 at 2.4 A Resolution Authors: Xia, Z.X. / Mathews, F.S. #2: ![]() Title: Isolation and Characterization of the Flavin-binding Domain of Flavocytochrome b2 Expressed Independently in Escherichia coli Authors: Blame, A. / Brunt, C.E. / Pallister, R.L. / Chapman, S.K. / Reid, G.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 173.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 136.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 34.1 KB | Display | |
Data in CIF | ![]() | 48.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kbiC ![]() 1fcbS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | The enzyme is a tetramer. |
-
Components
#1: Protein | Mass: 45691.297 Da / Num. of mol.: 2 / Fragment: FMN-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P00175, L-lactate dehydrogenase (cytochrome) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.58 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG, sodium citrate, ethylene glycol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Apr 9, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 37593 / Num. obs: 34160 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 5.2 / % possible all: 96.2 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Num. obs: 36688 / Num. measured all: 240788 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 96.2 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FCB Resolution: 2.5→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.157 | ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.5 Å |