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- PDB-2ft8: Structure of Cu(I)azurin, pH8, with the metal-binding loop sequen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ft8 | ||||||
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Title | Structure of Cu(I)azurin, pH8, with the metal-binding loop sequence "CTFPGHSALM" replaced with "CTPHPM" | ||||||
![]() | Azurin | ||||||
![]() | ELECTRON TRANSPORT / Blue copper-binding protein / greek-key beta-barrel. | ||||||
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 | ![]() ![]() | ||||||
![]() | Banfield, M.J. | ||||||
![]() | ![]() Title: Basic requirements for a metal-binding site in a protein: The influence of loop shortening on the cupredoxin azurin. Authors: Li, C. / Yanagisawa, S. / Martins, B.M. / Messerschmidt, A. / Banfield, M.J. / Dennison, C. #1: ![]() Title: Crystal structure analysis of oxidized Pseudomonas aeruginosa azurin at pH 5.5 and pH 9.0. A pH-induced conformational transition involves a peptide bond flip Authors: Nar, H. / Messerschmidt, A. / Huber, R. / van de Kamp, M. / Canters, G.W. #2: Journal: J.Am.Chem.Soc. / Year: 2004 Title: Loop-contraction mutagenesis of type 1 copper sites Authors: Yanagisawa, S. / Dennison, C. #3: ![]() Title: Crystal structure analysis and refinement at AT 2.15 A resolution of amicyanin, a type I blue copper protein, from Thiobacillus versutus Authors: Romero, A. / Nar, H. / Huber, R. / Messerschmidt, A. / Kalverda, A.P. / Canters, G.W. / Durley, R. / Mathews, F.S. | ||||||
History |
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Remark 999 | SEQUENCE Amino acid sequence CTFPGHSALM, involving residues 132 to 141 in the amino acid database ...SEQUENCE Amino acid sequence CTFPGHSALM, involving residues 132 to 141 in the amino acid database was replaced with the sequence CTPHPM in the deposition |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.9 KB | Display | ![]() |
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PDB format | ![]() | 50.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 412.9 KB | Display | ![]() |
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Full document | ![]() | 413.2 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 11.5 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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1 |
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Unit cell |
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Details | The biological assembly is monomeric (as found in the asymmetric unit) |
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Components
#1: Protein | Mass: 13583.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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: 1.87 Å3/Da / Density % sol: 34.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1MM MES, 20% PEG6000, 0.2M LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 16, 2005 |
Radiation | Monochromator: double Si(III) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→42.8 Å / Num. all: 15561 / Num. obs: 15561 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.55→1.63 Å / % possible obs: 97.7 % / Redundancy: 8 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.2 / Num. measured all: 17358 / Num. unique all: 2162 / Num. unique obs: 2162 / Rsym value: 0.358 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: Direct refinement from refined AZAMI-F Cu(II) structure Resolution: 1.55→42.8 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.863 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.105 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS BUT NOT OUTPUT TO THE COORDINATE FILE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.206 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→42.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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