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- PDB-1a8z: STRUCTURE DETERMINATION OF A 16.8KDA COPPER PROTEIN RUSTICYANIN A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1a8z | ||||||
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Title | STRUCTURE DETERMINATION OF A 16.8KDA COPPER PROTEIN RUSTICYANIN AT 2.1A RESOLUTION USING ANOMALOUS SCATTERING DATA WITH DIRECT METHODS | ||||||
![]() | RUSTICYANIN | ||||||
![]() | ELECTRON TRANSPORT / DIRECT METHODS / SAS / MEDIUM RESOLUTION / METALLOPROTEIN / COPPER PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Harvey, I. / Hao, Q. / Duke, E.M.H. / Ingledew, W.J. / Hasnain, S.S. | ||||||
![]() | ![]() Title: Structure determination of a 16.8 kDa copper protein at 2.1 A resolution using anomalous scattering data with direct methods. Authors: Harvey, I. / Hao, Q. / Duke, E.M. / Ingledew, W.J. / Hasnain, S.S. #1: ![]() Title: Oasis-A Computer Program for Breaking the Phase Ambiguity in Oas or Sir Protein Data Authors: Hao, Q. / Gu, Y.X. / Zheng, C.D. / Fan, H.F. #2: ![]() Title: Multiple Wavelength Anomalous Diffraction (MAD) Crystal Structure of Rusticyanin: A Highly Oxidizing Cupredoxin with Extreme Acid Stability Authors: Walter, R.L. / Ealick, S.E. / Friedman, A.M. / Blake II, R.C. / Proctor, P. / Shoham, M. #3: ![]() Title: Complete 13C Assignments for Recombinant Cu(I) Rusticyanin. Prediction of Secondary Structure from Patterns of Chemical Shifts Authors: Toy-Palmer, A. / Prytulla, S. / Dyson, H.J. #4: ![]() Title: X-Ray Absorption Studies and Homology Modeling Define the Structural Features that Specify the Nature of the Copper Site in Rusticyanin Authors: Grossmann, J.G. / Ingledew, W.J. / Harvey, I. / Strange, R.W. / Hasnain, S.S. #5: ![]() Title: Crystallization and Preliminary X-Ray Crystallographic Studies of Rusticyanin from Thiobacillus Ferrooxidans Authors: Djebli, A. / Proctor, P. / Blake II, R.C. / Shoham, M. #6: ![]() Title: Amino Acid Sequence of the Blue Copper Protein Rusticyanin from Thiobacillus Ferrooxidans Authors: Ronk, M. / Shively, J.E. / Shute, E.A. / Blake II, R.C. #8: ![]() Title: The Purification and Some Properties of Rusticyanin, a Blue Copper Protein Involved in Iron(II) Oxidation from Thiobacillus Ferro-Oxidans Authors: Cox, J.C. / Boxer, D.H. #9: ![]() Title: The Respiratory Chain of Thiobacillus Ferrooxidans: The Reduction of Cytochromes by Fe2+ and the Preliminary Characterization of Rusticyanin a Novel "Blue" Copper Protein Authors: Cobley, J.G. / Haddock, B.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 | ![]() | 43.3 KB | Display | ![]() |
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PDB format | ![]() | 29.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 410 KB | Display | ![]() |
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Full document | ![]() | 410.9 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
#1: Protein | Mass: 16408.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: REDUCED FORM (CU(I)) / Source: (natural) ![]() |
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#2: Chemical | ChemComp-CU1 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 38 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 3.8 Details: SIMILAR TO THOSE DESCRIBED IN DJEBLI ET AL., J. MOL. BIOL. 229, 581 (1992)., pH 3.8 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 4, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.376 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 7898 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.029 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 6.1 / Rsym value: 0.066 / % possible all: 91.9 |
Reflection | *PLUS Num. measured all: 80752 |
Reflection shell | *PLUS % possible obs: 91.9 % |
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Processing
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Refinement | Method to determine structure: ANOMALOUS SCATTERING, DIRECT METHODS Resolution: 2.1→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 14.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.19 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.251 |