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Open data
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Basic information
Entry | Database: PDB / ID: 5wr6 | ||||||
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Title | Thermolysin, liganded form with cryo condition 2 | ||||||
![]() | Thermolysin | ||||||
![]() | HYDROLASE / X-ray free-electron laser / Serial femtosecond crystallography / Microcrystal / Structure-based drug design | ||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kunishima, N. / Naitow, H. / Matsuura, Y. | ||||||
![]() | ![]() Title: Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation Authors: Naitow, H. / Matsuura, Y. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / Yabashi, M. / Tanaka, R. / Tanaka, T. / Sugahara, M. / Kobayashi, J. / Nango, E. / Iwata, S. / Kunishima, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.7 KB | Display | ![]() |
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PDB format | ![]() | 64.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 727.9 KB | Display | ![]() |
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Full document | ![]() | 728.6 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wr2C ![]() 5wr3C ![]() 5wr4C ![]() 5wr5C ![]() 4ow3S C: citing same article ( 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Fragment: UNP residues 236-551 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nprS, nprM / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-NX6 / | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG2000MME, MES, CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.5 Å / Num. obs: 14641 / % possible obs: 96 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.17 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 3.6 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4OW3 Resolution: 2.3→40.2 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / Phase error: 16.53
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Displacement parameters | Biso mean: 22.41 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→40.2 Å
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LS refinement shell | Resolution: 2.3→2.48 Å
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