+Open data
-Basic information
Entry | Database: PDB / ID: 5un3 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Tetragonal thermolysin (295 K) in the presence of 50% xylose | |||||||||
Components | Thermolysin | |||||||||
Keywords | HYDROLASE / zinc protease / alpha/beta | |||||||||
Function / homology | Function and homology information thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus thermoproteolyticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.60004437941 Å | |||||||||
Authors | Juers, D. | |||||||||
Funding support | United States, 1items
| |||||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5un3.cif.gz | 167.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5un3.ent.gz | 109.4 KB | Display | PDB format |
PDBx/mmJSON format | 5un3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5un3_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5un3_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 5un3_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 5un3_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/5un3 ftp://data.pdbj.org/pub/pdb/validation_reports/un/5un3 | 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 (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 6 molecules A
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thermoproteolyticus (bacteria) Gene: npr / Production host: Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin |
---|---|
#5: Sugar | ChemComp-XYP / |
-Non-polymers , 4 types, 260 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.19 % |
---|---|
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 |
---|---|
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.60004437941→20.2103390027 Å / SU ML: 0.206163723556 / Cross valid method: FREE R-VALUE / σ(F): 0.599035467022 / Phase error: 21.2053246406 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|