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- PDB-1kss: Crystal Structure of His505Ala Mutant Flavocytochrome c3 from She... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kss | |||||||||
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Title | Crystal Structure of His505Ala Mutant Flavocytochrome c3 from Shewanella frigidimarina | |||||||||
![]() | flavocytochrome c | |||||||||
![]() | OXIDOREDUCTASE / flavocytochrome / fumarate reductase / H505A | |||||||||
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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.8 KB | Display | ![]() |
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PDB format | ![]() | 116.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ksuC ![]() 1qjdS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60560.172 Da / Num. of mol.: 1 / Mutation: H505A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q02469, UniProt: P0C278*PLUS, succinate dehydrogenase |
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-Non-polymers , 5 types, 1104 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 | ChemComp-NA / | ||||||
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#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-FAD / | #5: Chemical | ChemComp-FUM / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.59 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG8000, NaCl, TrisHCl, sodium fumarate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 58239 / Num. obs: 58239 / % possible obs: 95.4 % / Redundancy: 5.46 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 4.9 / Num. unique all: 5691 / % possible all: 93.8 |
Reflection | *PLUS Num. measured all: 318233 / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Rmerge(I) obs: 0.185 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QJD Resolution: 1.8→10 Å / SU B: 2.31756 / SU ML: 0.0741 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.11746 / ESU R Free: 0.11967 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 17 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.877 Å
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor all: 0.1564 / Rfactor Rfree: 0.2061 / Rfactor Rwork: 0.1564 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.237 / Rfactor Rwork: 0.163 |