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- PDB-6sr1: X-ray pump X-ray probe on lysozyme.Gd nanocrystals: 35 fs time delay -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sr1 | ||||||
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Title | X-ray pump X-ray probe on lysozyme.Gd nanocrystals: 35 fs time delay | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / Radiation damage / SERIAL femtosecond CRYSTALLOGRAPHY / X-ray FREE-ELECTRON LASER / time-resolved crystallography | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Kloos, M. / Gorel, A. / Nass, K. | ||||||
![]() | ![]() Title: Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses. Authors: Nass, K. / Gorel, A. / Abdullah, M.M. / V Martin, A. / Kloos, M. / Marinelli, A. / Aquila, A. / Barends, T.R.M. / Decker, F.J. / Bruce Doak, R. / Foucar, L. / Hartmann, E. / Hilpert, M. / ...Authors: Nass, K. / Gorel, A. / Abdullah, M.M. / V Martin, A. / Kloos, M. / Marinelli, A. / Aquila, A. / Barends, T.R.M. / Decker, F.J. / Bruce Doak, R. / Foucar, L. / Hartmann, E. / Hilpert, M. / Hunter, M.S. / Jurek, Z. / Koglin, J.E. / Kozlov, A. / Lutman, A.A. / Kovacs, G.N. / Roome, C.M. / Shoeman, R.L. / Santra, R. / Quiney, H.M. / Ziaja, B. / Boutet, S. / Schlichting, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.3 KB | Display | ![]() |
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PDB format | ![]() | 29.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6sr0C ![]() 6sr2C ![]() 6sr3C ![]() 6sr4C ![]() 6sr5C ![]() 6srjC ![]() 6srkC ![]() 6srlC ![]() 6sroC ![]() 6srpC ![]() 6srqC ![]() 4n5rS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16257.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Cysteine residues were modeled by alanines and a non-covalently bound sulphur during refinement Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 34 molecules ![](data/chem/img/GD.gif)
![](data/chem/img/DO3.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DO3.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.11 % / Description: nanocrystals |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 3 Details: 20 % NACL, 6 % PEG 6000, 0.1 M SODIUM acetate pH 3.0 Temp details: ice cold solutions |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Feb 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.75 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→22.81 Å / Num. obs: 5315 / % possible obs: 100 % / Redundancy: 1 % / Biso Wilson estimate: 27.5 Å2 / CC1/2: 0.98 / R split: 0.084 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.32→2.36 Å / Mean I/σ(I) obs: 10.8 / Num. unique obs: 436 / CC1/2: 0.979 / R split: 0.085 |
Serial crystallography measurement | Focal spot size: 0.025 µm2 / Pulse duration: 15 fsec. / Pulse energy: 500 µJ / Pulse photon energy: 7.07 keV / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Description: GDVN injection / Method: injection |
Serial crystallography data reduction | Frames indexed: 16000 / Lattices indexed: 16000 |
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Processing
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Refinement |