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Open data
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Basic information
Entry | Database: PDB / ID: 1yai | ||||||
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Title | X-RAY STRUCTURE OF A BACTERIAL COPPER,ZINC SUPEROXIDE DISMUTASE | ||||||
![]() | COPPER, ZINC SUPEROXIDE DISMUTASE | ||||||
![]() | OXIDOREDUCTASE / BETA-BARREL / METALLOENZYME / MACROMOLECULAR ASSEMBLY | ||||||
Function / homology | ![]() superoxide dismutase / superoxide dismutase activity / periplasmic space / copper ion binding / extracellular space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bourne, Y. / Redford, S.M. / Lo, T.P. / Tainer, J.A. / Getzoff, E.D. | ||||||
![]() | ![]() Title: Novel dimeric interface and electrostatic recognition in bacterial Cu,Zn superoxide dismutase. Authors: Bourne, Y. / Redford, S.M. / Steinman, H.M. / Lepock, J.R. / Tainer, J.A. / Getzoff, E.D. #1: ![]() Title: Crystallographic Characterization of a Cu,Zn Superoxide Dismutase from Photobacterium Leiognathi Authors: Redford, S.M. / Mcree, D.E. / Getzoff, E.D. / Steinman, H.M. / Tainer, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.8 KB | Display | ![]() |
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PDB format | ![]() | 78.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 378 KB | Display | ![]() |
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Full document | ![]() | 385.2 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sodS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.20969, -0.65398, -0.72687), Vector: |
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Components
#1: Protein | Mass: 15801.800 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | IN ALL THREE CHAINS, ARG 144 IS THE CATALYTICALLY IMPORTANT RESIDUE FOR SUPEROXIDE ANION ...IN ALL THREE CHAINS, ARG 144 IS THE CATALYTICA | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: 42% MPD, 60 MM POTASSIUM PHOSPHATE, PH 6.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion / Details: macroseeding | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jul 20, 1991 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.9 Å / Num. obs: 116490 / % possible obs: 83 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.049 |
Reflection | *PLUS Num. obs: 30277 / Num. measured all: 116490 / Rmerge(I) obs: 0.049 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3SOD Resolution: 1.9→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: X-PLOR ALSO USED
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 204 Å2 / ksol: 0.65 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5EB / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.149 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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