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Open data
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Basic information
Entry | Database: PDB / ID: 5x31 | ||||||
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Title | Pseudoazurin from Alcaligenes faecalis (space group P65) | ||||||
![]() | Pseudoazurin | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fukuda, Y. / Mizohata, E. / Inoue, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: New molecular packing in a crystal of pseudoazurin from Alcaligenes faecalis: a double-helical arrangement of blue copper Authors: Fukuda, Y. / Mizohata, E. / Inoue, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.1 KB | Display | ![]() |
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PDB format | ![]() | 44 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1pazS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13672.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.8 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 32.5-37.5% Polyethylene glycol 8000, 1.5 micro L of protein solution and 1.5 micro L reservoir |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→50 Å / Num. obs: 8741 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.076 / Rrim(I) all: 0.145 / Χ2: 1.059 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 447 / CC1/2: 0.953 / Rpim(I) all: 0.141 / Rrim(I) all: 0.279 / Χ2: 0.734 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1PAZ Resolution: 2.6→36.92 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.89 / SU B: 0.005 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.324 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||
Displacement parameters | Biso mean: 24.483 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→36.92 Å
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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