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Open data
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Basic information
Entry | Database: PDB / ID: 1jze | ||||||
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Title | Pseudomonas aeruginosa Azurin Ru(bpy)2(im)(His83) | ||||||
![]() | azurin | ||||||
![]() | ELECTRON TRANSPORT / Blue-copper / Electron Transfer / Ruthenium | ||||||
Function / homology | ![]() transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Crane, B.R. / Di Bilio, A.J. / Winkler, J.R. / Gray, H.B. | ||||||
![]() | ![]() Title: Electron tunneling in single crystals of Pseudomonas aeruginosa azurins. Authors: Crane, B.R. / Di Bilio, A.J. / Winkler, J.R. / Gray, H.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.7 KB | Display | ![]() |
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PDB format | ![]() | 29.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 584.4 KB | Display | ![]() |
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Full document | ![]() | 589.1 KB | Display | |
Data in XML | ![]() | 5.1 KB | Display | |
Data in CIF | ![]() | 7.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jzfC ![]() 1jzgC ![]() 1jzhC ![]() 1jziC ![]() 1jzjC ![]() 1bexS 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 biological assembly is a monomer |
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Components
#1: Protein | Mass: 13961.799 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-DRU / | #4: Chemical | ChemComp-LRU / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.45 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / PH range low: 8 / PH range high: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 8, 1998 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→26 Å / Num. all: 13982 / Num. obs: 13982 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.05 / Net I/σ(I): 34 |
Reflection shell | Resolution: 1.6→1.66 Å / Mean I/σ(I) obs: 2.9 / Num. unique all: 688 / Rsym value: 0.213 / % possible all: 46.1 |
Reflection | *PLUS Rmerge(I) obs: 0.05 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BEX Resolution: 1.6→26.72 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 342245.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.3619 Å2 / ksol: 0.318763 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→26.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.079 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 8 % / Rfactor obs: 0.249 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.386 / % reflection Rfree: 8 % / Rfactor Rwork: 0.32 |