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Yorodumi- PDB-6sr4: X-ray pump X-ray probe on lysozyme.Gd nanocrystals: 112 fs time delay -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sr4 | ||||||
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Title | X-ray pump X-ray probe on lysozyme.Gd nanocrystals: 112 fs time delay | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Radiation damage / SERIAL femtosecond CRYSTALLOGRAPHY / X-ray FREE-ELECTRON LASER / time-resolved crystallography | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kloos, M. / Gorel, A. / Nass, K. | ||||||
Citation | Journal: Nat Commun / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sr4.cif.gz | 45.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sr4.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 6sr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sr/6sr4 ftp://data.pdbj.org/pub/pdb/validation_reports/sr/6sr4 | HTTPS FTP |
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-Related structure data
Related structure data | 6sr0C 6sr1C 6sr2C 6sr3C 6sr5C 6srjC 6srkC 6srlC 6sroC 6srpC 6srqC 4n5rS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 as alanines and non-covalent sulfur atom. the protein contains a Gd compound Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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-Non-polymers , 5 types, 34 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.11 % |
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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: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.75 Å |
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: 39.1 Å2 / CC1/2: 0.978 / R split: 0.091 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.32→2.36 Å / Mean I/σ(I) obs: 7.1 / Num. unique obs: 436 / CC1/2: 0.895 / R split: 0.18 |
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: GDNV injection / Method: injection |
Serial crystallography data reduction | Frames indexed: 16000 / Lattices indexed: 16000 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4n5r Resolution: 2.3→22.81 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.876 / SU B: 7.88 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.518 / ESU R Free: 0.299 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY The submitted coordinates represent the mean of 100 coordinate sets obtained by refining against 100 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY The submitted coordinates represent the mean of 100 coordinate sets obtained by refining against 100 different integrated diffraction intensity datasets obtained by jackknife resampling of the diffraction snapshots. The coordinate header originates from one of the individual refinements. cysteine residues were modeled as alanines and non-covalently attached sulphur atoms.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.46 Å2 / Biso mean: 33.959 Å2 / Biso min: 22.97 Å2
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Refinement step | Cycle: final / Resolution: 2.3→22.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.302→2.361 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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