[English] 日本語
![](img/lk-miru.gif)
- PDB-1ksu: Crystal Structure of His505Tyr Mutant Flavocytochrome c3 from She... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ksu | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of His505Tyr Mutant Flavocytochrome c3 from Shewanella frigidimarina | |||||||||
![]() | flavocytochrome c | |||||||||
![]() | OXIDOREDUCTASE / flavocytochrome c3 / fumarate reductase / H505Y | |||||||||
Function / homology | ![]() fumarate reductase (cytochrome) / fumarate reductase (quinol) / : / anaerobic electron transport chain / anaerobic respiration / steroid metabolic process / FMN binding / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity ...fumarate reductase (cytochrome) / fumarate reductase (quinol) / : / anaerobic electron transport chain / anaerobic respiration / steroid metabolic process / FMN binding / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / oxidoreductase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pankhurst, K.L. / Mowat, C.G. / Miles, C.S. / Leys, D. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K. | |||||||||
![]() | ![]() Title: Role of His505 in the soluble fumarate reductase from Shewanella frigidimarina. Authors: Pankhurst, K.L. / Mowat, C.G. / Miles, C.S. / Leys, D. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 283.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 220.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1kssC ![]() 1qjdS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60652.273 Da / Num. of mol.: 2 / Mutation: H505Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q02469, UniProt: P0C278*PLUS, succinate dehydrogenase |
---|
-Non-polymers , 5 types, 1881 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/FUM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/FUM.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-HEM / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.67 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG8000, TrisHCl, NaCl, sodium fumarate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 7, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8459 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 536347 / Num. obs: 77608 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 3.32 / Num. unique all: 7631 / % possible all: 97.9 |
Reflection | *PLUS Num. measured all: 536347 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS Rmerge(I) obs: 0.223 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QJD Resolution: 2→15 Å / SU B: 3.9701 / SU ML: 0.11326 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.19912 / ESU R Free: 0.18659 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 16 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.091 Å
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor all: 0.167 / Rfactor Rfree: 0.2386 / Rfactor Rwork: 0.167 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.221 / Rfactor Rwork: 0.154 |