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Open data
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Basic information
Entry | Database: PDB / ID: 5un3 | |||||||||
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Title | Tetragonal thermolysin (295 K) in the presence of 50% xylose | |||||||||
![]() | Thermolysin | |||||||||
![]() | HYDROLASE / zinc protease / alpha/beta | |||||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Juers, D. | |||||||||
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 | ![]() | 167.2 KB | Display | ![]() |
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PDB format | ![]() | 109.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.4 KB | Display | ![]() |
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Full document | ![]() | 437.1 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 24 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uu7C ![]() 5uu8C ![]() 5uu9C ![]() 5uuaC ![]() 5uubC ![]() 5uucC ![]() 5uudC ![]() 5uueC ![]() 6avlC ![]() 6b6nC ![]() 6b6oC ![]() 6b6pC ![]() 6b6qC ![]() 6b6rC ![]() 6b6sC ![]() 6b6tC ![]() 6d5nC ![]() 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 6 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 genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: npr / Production host: ![]() ![]() |
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#5: Sugar | ChemComp-XYP / |
-Non-polymers , 4 types, 260 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.19 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: Drop: 45% DMSO, 0.5 M ZnCl2, 50 mg/mL protein Well: ~2 M AmSO4 |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Oct 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20.2 Å / % possible obs: 99.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 17.8881911535 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.7 % / CC1/2: 0.258 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.9817184503 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.60004437941→20.2103390027 Å
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Refine LS restraints |
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LS refinement shell |
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