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- PDB-8cwd: 20ns Temperature-Jump (Dark1) XFEL structure of Lysozyme Bound to... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cwd | |||||||||
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Title | 20ns Temperature-Jump (Dark1) XFEL structure of Lysozyme Bound to N,N'-diacetylchitobiose | |||||||||
![]() | Lysozyme C | |||||||||
![]() | HYDROLASE / lysozyme / temperature-jump / 20ns / dark1 / xfel / inhibitor / diacetylchitobiose | |||||||||
Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wolff, A.M. / Thompson, M.C. / Fraser, J.S. / Nango, E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography. Authors: Wolff, A.M. / Nango, E. / Young, I.D. / Brewster, A.S. / Kubo, M. / Nomura, T. / Sugahara, M. / Owada, S. / Barad, B.A. / Ito, K. / Bhowmick, A. / Carbajo, S. / Hino, T. / Holton, J.M. / Im, ...Authors: Wolff, A.M. / Nango, E. / Young, I.D. / Brewster, A.S. / Kubo, M. / Nomura, T. / Sugahara, M. / Owada, S. / Barad, B.A. / Ito, K. / Bhowmick, A. / Carbajo, S. / Hino, T. / Holton, J.M. / Im, D. / O'Riordan, L.J. / Tanaka, T. / Tanaka, R. / Sierra, R.G. / Yumoto, F. / Tono, K. / Iwata, S. / Sauter, N.K. / Fraser, J.S. / Thompson, M.C. #1: ![]() Title: Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography Authors: Wolff, A.M. / Nango, E. / Young, I.D. / Brewster, A.S. / Kubo, M. / Nomura, T. / Sugahara, M. / Owada, S. / Barad, B.A. / Ito, K. / Bhowmick, A. / Carbajo, S. / Hino, T. / Holton, J.M. / Im, ...Authors: Wolff, A.M. / Nango, E. / Young, I.D. / Brewster, A.S. / Kubo, M. / Nomura, T. / Sugahara, M. / Owada, S. / Barad, B.A. / Ito, K. / Bhowmick, A. / Carbajo, S. / Hino, T. / Holton, J.M. / Im, D. / O'Riordan, L.J. / Tanaka, T. / Tanaka, R. / Sierra, R.G. / Yumoto, F. / Tono, K. / Iwata, S. / Sauter, N.K. / Fraser, J.S. / Thompson, M.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.9 KB | Display | ![]() |
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PDB format | ![]() | 69.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8cvuC ![]() 8cvvC ![]() 8cvwC ![]() 8cw0C ![]() 8cw1C ![]() 8cw3C ![]() 8cw5C ![]() 8cw6C ![]() 8cw7C ![]() 8cw8C ![]() 8cwbC ![]() 8cwcC ![]() 8cweC ![]() 8cwfC ![]() 8cwgC ![]() 8cwhC ![]() 1ieeS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
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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: 14331.160 Da / Num. of mol.: 1 / Fragment: lyzozyme / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose | ||||||
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.2 % |
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Crystal grow | Temperature: 291 K / Method: batch mode / pH: 3 Details: Lysozyme-inhibitor complex [20 mg/ml lysozyme plus 10 mg/ml N,N'-diacetylchitobiose dissolved in 0.1 M sodium acetate at pH 3.0] mixed with precipitant [28% (w/v) NaCl, 8% (w/v) PEG6000 and ...Details: Lysozyme-inhibitor complex [20 mg/ml lysozyme plus 10 mg/ml N,N'-diacetylchitobiose dissolved in 0.1 M sodium acetate at pH 3.0] mixed with precipitant [28% (w/v) NaCl, 8% (w/v) PEG6000 and 0.1 M sodium acetate at pH 3.0] in a 1:1 ratio |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MPCCD / Detector: CCD / Date: Jul 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2468 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→30.74 Å / Num. obs: 3283906 / % possible obs: 99.98 % / Redundancy: 170.64 % / Biso Wilson estimate: 15.35 Å2 / CC1/2: 0.993 / Net I/σ(I): 11.746 |
Reflection shell | Resolution: 1.48→1.51 Å / Num. unique obs: 33942 / CC1/2: 0.841 |
Serial crystallography sample delivery | Method: injection |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1iee Resolution: 1.48→30.74 Å / SU ML: 0.1081 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.4262 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: 19.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→30.74 Å
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Refine LS restraints |
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LS refinement shell |
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