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Open data
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Basic information
Entry | Database: PDB / ID: 6d5n | |||||||||
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Title | Hexagonal thermolysin (295) in the presence of 50% xylose | |||||||||
![]() | Thermolysin | |||||||||
![]() | HYDROLASE / zinc protease | |||||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Juers, D.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order. Authors: Juers, D.H. / Farley, C.A. / Saxby, C.P. / Cotter, R.A. / Cahn, J.K.B. / Holton-Burke, R.C. / Harrison, K. / Wu, Z. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.1 KB | Display | ![]() |
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PDB format | ![]() | 102.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.8 KB | Display | ![]() |
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Full document | ![]() | 458.9 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5un3C ![]() 5uu7C ![]() 5uu8C ![]() 5uu9C ![]() 5uuaC ![]() 5uubC ![]() 5uucC ![]() 5uudC ![]() 5uueC ![]() 6avlC ![]() 6b6nC ![]() 6b6oC ![]() 6b6pC ![]() 6b6qC ![]() 6b6rC ![]() 6b6sC ![]() 6b6tC ![]() 6d5oC ![]() 6d5pC ![]() 6d5qC ![]() 6d5rC ![]() 6d5sC ![]() 6d5tC ![]() 6d5uC ![]() 6d6eC ![]() 6d6fC ![]() 6d6gC ![]() 6d6hC ![]() 6dzfC C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 3 molecules A![](data/chem/img/XYP.gif)
![](data/chem/img/XYP.gif)
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#6: Sugar |
-Non-polymers , 5 types, 147 molecules ![](data/chem/img/VAL.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-VAL / | ||
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#3: Chemical | ChemComp-LYS / | ||
#4: Chemical | ChemComp-ZN / | ||
#5: Chemical | ChemComp-CA / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.33 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: Protein: 100 mg/mL in 45% DMSO Well: 2 M AmSO4 |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Jul 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→13.86 Å / Num. obs: 23812 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 19.6315777022 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.142 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2→2.11 Å / CC1/2: 0.736 |
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Processing
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Refinement | Resolution: 2.00003665634→13.8519097476 Å / SU ML: 0.213793487267 / Cross valid method: FREE R-VALUE / σ(F): 1.33721327711 / Phase error: 17.3279762667
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9275337172 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.00003665634→13.8519097476 Å
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Refine LS restraints |
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LS refinement shell |
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