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Yorodumi- PDB-5uvj: Serial Millisecond Crystallography of Membrane and Soluble Protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uvj | |||||||||||||||||||||||||||
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Title | Serial Millisecond Crystallography of Membrane and Soluble Protein Micro-crystals using Synchrotron Radiation | |||||||||||||||||||||||||||
Components | Lysozyme C | |||||||||||||||||||||||||||
Keywords | HYDROLASE | |||||||||||||||||||||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||||||||||||||||||||
Authors | Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. ...Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / Nagaratnam, N. / Roy-Chowdhury, S. / Coe, J. / Subramanian, G. / Schaffer, A. / James, D. / Ketawala, G. / Venugopalan, N. / Xu, S. / Corcoran, S. / Ferguson, D. / Weierstall, U. / Spence, J.C.H. / Cherezov, V. / Fromme, P. / Fischetti, R.F. / Liu, W. | |||||||||||||||||||||||||||
Funding support | United States, 8items
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Citation | Journal: IUCrJ / Year: 2017 Title: Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation. Authors: Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / ...Authors: Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / Nagaratnam, N. / Roy-Chowdhury, S. / Coe, J. / Subramanian, G. / Schaffer, A. / James, D. / Ketwala, G. / Venugopalan, N. / Xu, S. / Corcoran, S. / Ferguson, D. / Weierstall, U. / Spence, J.C.H. / Cherezov, V. / Fromme, P. / Fischetti, R.F. / Liu, W. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uvj.cif.gz | 40.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uvj.ent.gz | 25.9 KB | Display | PDB format |
PDBx/mmJSON format | 5uvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/5uvj ftp://data.pdbj.org/pub/pdb/validation_reports/uv/5uvj | HTTPS FTP |
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-Related structure data
Related structure data | 5uviC 5uvkC 5uvlC 4zixS 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
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme | ||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.69 % |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 3 Details: 18 % (w/v) NaCl, 6 % (v/v) PEG 6000, 1 M sodium acetate pH 3.0 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→35 Å / Num. obs: 7164 / % possible obs: 99.79 % / Redundancy: 873.3 % / CC1/2: 0.978 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 0.4 % / CC1/2: 0.436 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZIX Resolution: 2.05→35 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.809 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.203 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→35 Å
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Refine LS restraints |
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