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Open data
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Basic information
Entry | Database: PDB / ID: 1jvo | ||||||
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Title | Azurin dimer, crosslinked via disulfide bridge | ||||||
![]() | Azurin | ||||||
![]() | ELECTRON TRANSPORT / cupredoxin / electron transfer / covalent crosslink | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | van Amsterdam, I.M.C. / Ubbink, M. / Einsle, O. / Messerschmidt, A. / Merli, A. / Cavazzini, D. / Rossi, G.L. / Canters, G.W. | ||||||
![]() | ![]() Title: Dramatic modulation of electron transfer in protein complexes by crosslinking Authors: van Amsterdam, I.M.C. / Ubbink, M. / Einsle, O. / Messerschmidt, A. / Merli, A. / Cavazzini, D. / Rossi, G.L. / Canters, G.W. #1: ![]() Title: Effects of Dimerization on Protein Electron Transfer Authors: van Amsterdam, I.M.C. / Ubbink, M. / Jeuken, L.J.C. / Verbeet, M.P. / Einsle, O. / Messerschmidt, A. / Canters, G.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 282.9 KB | Display | ![]() |
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PDB format | ![]() | 241.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.8 KB | Display | ![]() |
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Full document | ![]() | 451.2 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 47.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | FOUR MONOMERS GENERATE A TETRAMER ACTIVE IN INTERMOLECULAR ELECTRON TRANSFER. THE ASYMMETRIC UNIT CONTAINS THREE SUCH TETRAMERS. PROGRAM PISA DOES NOT PREDICT THOSE ASSEMBLIES BECAUSE THE INDIVIDUAL INTERMOLECULAR DISULFIDE BOND DOES NOT CREATE SUFFICIENT BURIED AREA. |
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Components
#1: Protein | Mass: 13950.839 Da / Num. of mol.: 12 / Fragment: Azurin / Mutation: N42C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CU / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.73 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 8000, Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 293K, temperature 293.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
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: CCD / Date: Oct 9, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. all: 41247 / Num. obs: 35555 / % possible obs: 86.2 % / Observed criterion σ(I): 3 / Redundancy: 1.9 % / Biso Wilson estimate: 60.1 Å2 / Rsym value: 0.101 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 3588 / Rsym value: 0.404 / % possible all: 88.2 |
Reflection | *PLUS Num. obs: 42605 / Rmerge(I) obs: 0.108 |
Reflection shell | *PLUS % possible obs: 86.4 % / Rmerge(I) obs: 0.484 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.75→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.239 / Rfactor Rfree: 0.293 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.34 |