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- PDB-7bhl: Crystal structure of hen egg white lysozyme using drop-on-drop SF... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bhl | ||||||||||||
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Title | Crystal structure of hen egg white lysozyme using drop-on-drop SFX method - 0.2 s mixing with N-acetyl-D-glucosamine. | ||||||||||||
![]() | Lysozyme | ||||||||||||
![]() | HYDROLASE / lysozyme / SFX / XFEL | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Butryn, A. / Orville, A.M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography. Authors: Butryn, A. / Simon, P.S. / Aller, P. / Hinchliffe, P. / Massad, R.N. / Leen, G. / Tooke, C.L. / Bogacz, I. / Kim, I.S. / Bhowmick, A. / Brewster, A.S. / Devenish, N.E. / Brem, J. / Kamps, J. ...Authors: Butryn, A. / Simon, P.S. / Aller, P. / Hinchliffe, P. / Massad, R.N. / Leen, G. / Tooke, C.L. / Bogacz, I. / Kim, I.S. / Bhowmick, A. / Brewster, A.S. / Devenish, N.E. / Brem, J. / Kamps, J.J.A.G. / Lang, P.A. / Rabe, P. / Axford, D. / Beale, J.H. / Davy, B. / Ebrahim, A. / Orlans, J. / Storm, S.L.S. / Zhou, T. / Owada, S. / Tanaka, R. / Tono, K. / Evans, G. / Owen, R.L. / Houle, F.A. / Sauter, N.K. / Schofield, C.J. / Spencer, J. / Yachandra, V.K. / Yano, J. / Kern, J.F. / Orville, A.M. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.9 KB | Display | ![]() |
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PDB format | ![]() | 27.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7bh3C ![]() 7bh4C ![]() 7bh5C ![]() 7bh6C ![]() 7bh7C ![]() 7bhkC ![]() 7bhmC ![]() 7bhnC ![]() 4etaS 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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1 |
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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 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.25 % |
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Crystal grow | Temperature: 295 K / Method: batch mode Details: 1 M citric acid, 20% (w/v) NaCl, 5% (w/v) PEG 6000, pH 3.0 |
-Data collection
Diffraction | Mean temperature: 308 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→55.72 Å / Num. obs: 21782 / % possible obs: 100 % / Redundancy: 52.84 % / Biso Wilson estimate: 23.47 Å2 / CC1/2: 0.94 / R split: 0.2 / Net I/σ(I): 55.75 |
Reflection shell | Resolution: 1.45→1.475 Å / Mean I/σ(I) obs: 0.497 / Num. unique obs: 1056 / CC1/2: 0.03 / R split: 0.129 / % possible all: 100 |
Serial crystallography sample delivery | Description: acoustic droplet ejection / Method: injection |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ETA Resolution: 1.45→34.23 Å / SU ML: 0.2567 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8129 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: 27.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→34.23 Å
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Refine LS restraints |
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LS refinement shell |
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