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- PDB-3f7l: X-ray Crystal Structure of Alvinella pompejana Cu,Zn Superoxide D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f7l | ||||||
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Title | X-ray Crystal Structure of Alvinella pompejana Cu,Zn Superoxide Dismutase | ||||||
![]() | Copper,Zinc Superoxide Dismutase | ||||||
![]() | OXIDOREDUCTASE / OXIDOREDUCTASE (SUPEROXIDE ACCEPTOR) / superoxide dismutase / Greek key beta-barrel / amyloid filaments / ALS / FALS / Lou Gehrig's disease / amyotrophic lateral sclerosis / Alvinella pompejana / Pompeii worm / eukaryotic thermophile / thermostable protein | ||||||
Function / homology | ![]() superoxide dismutase / superoxide dismutase activity / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shin, D.S. / DiDonato, M. / Barondeau, D.P. / Getzoff, E.D. / Tainer, J.A. | ||||||
![]() | ![]() Title: Superoxide Dismutase from the Eukaryotic Thermophile Alvinella pompejana: Structures, Stability, Mechanism, and Insights into Amyotrophic Lateral Sclerosis. Authors: Shin, D.S. / Didonato, M. / Barondeau, D.P. / Hura, G.L. / Hitomi, C. / Berglund, J.A. / Getzoff, E.D. / Cary, S.C. / Tainer, J.A. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.4 KB | Display | ![]() |
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PDB format | ![]() | 67 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.9 KB | Display | ![]() |
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Full document | ![]() | 434 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f7kC ![]() 1pu0S C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Details | The second subunit of the dimer is generated by the operators y-x,y,1/2-z |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 15722.490 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 366 molecules ![](data/chem/img/CU1.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CU1 / | ||||
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#3: Chemical | ChemComp-CU / | ||||
#4: Chemical | ChemComp-ZN / | ||||
#5: Chemical | ChemComp-NA / | ||||
#6: Chemical | #7: Chemical | ChemComp-SO4 / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.95 % |
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Crystal grow | Temperature: 298 K / pH: 5.5 Details: 55% saturated ammonium sulfate, 100 mM Na citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 14, 2005 |
Radiation | Monochromator: SIBYLS KOHZU DUAL DOUBLE SI(111) CRYSTAL MONOCHROMATOR (DDCM) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 0.99→50 Å / Num. obs: 98085 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.068 / Net I/σ(I): 15.45 |
Reflection shell | Resolution: 0.99→1.03 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.503 / Rsym value: 0.291 / % possible all: 54 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PU0 Resolution: 0.99→45 Å / Num. parameters: 13842 / Num. restraintsaints: 16320 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 10 / Occupancy sum hydrogen: 1057.75 / Occupancy sum non hydrogen: 1454.94 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.99→45 Å
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Refine LS restraints |
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