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Open data
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Basic information
Entry | Database: PDB / ID: 7tc5 | ||||||
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Title | All Phe-Azurin variant - F15Y | ||||||
![]() | Azurin | ||||||
![]() | ELECTRON TRANSPORT / copper ion binding / cupredoxin / azurin / metal ion binding | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fedoretz-Maxwell, B.P. / Worrall, L.J. / Strynadka, N.C.J. / Warren, J.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Impact of Second Coordination Sphere Methionine-Aromatic Interactions in Copper Proteins. Authors: Fedoretz-Maxwell, B.P. / Shin, C.H. / MacNeil, G.A. / Worrall, L.J. / Park, R. / Strynadka, N.C.J. / Walsby, C.J. / Warren, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.4 KB | Display | ![]() |
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PDB format | ![]() | 48.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tc6C ![]() 4azuS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 13933.787 Da / Num. of mol.: 2 / Mutation: F15Y, W48F, Y72F, H83Q, Y108F, T124H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-NO3 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 mg/mL protein in 0.1 M NaOAc (pH 5.0), 26.5-29% PEG 4000, 100 mM lithium nitrate, 10 mM copper sulfate, and 100 mM tris (pH 8.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→44.6 Å / Num. obs: 45146 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2184 / CC1/2: 0.683 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4AZU Resolution: 1.45→41.97 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.596 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 81.13 Å2 / Biso mean: 23.548 Å2 / Biso min: 12.4 Å2
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Refinement step | Cycle: final / Resolution: 1.45→41.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.47 Å / Rfactor Rfree error: 0
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