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Yorodumi- PDB-5d5f: In meso in situ serial X-ray crystallography structure of lysozym... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d5f | ||||||
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Title | In meso in situ serial X-ray crystallography structure of lysozyme by bromine-SAD at 100 K | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information 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 | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Huang, C.-Y. / Olieric, V. / Diederichs, K. / Wang, M. / Caffrey, M. | ||||||
Funding support | Ireland, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Howe, N. / Vogeley, L. / Liu, X. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Kobilka, B. / Diederichs, K. / Wang, M. / Caffrey, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d5f.cif.gz | 40.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d5f.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 5d5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d5f_validation.pdf.gz | 651.5 KB | Display | wwPDB validaton report |
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Full document | 5d5f_full_validation.pdf.gz | 651.5 KB | Display | |
Data in XML | 5d5f_validation.xml.gz | 9 KB | Display | |
Data in CIF | 5d5f_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/5d5f ftp://data.pdbj.org/pub/pdb/validation_reports/d5/5d5f | HTTPS FTP |
-Related structure data
Related structure data | 5d52C 5d53C 5d54C 5d56C 5d57C 5d58C 5d59C 5d5aC 5d5bC 5d5cC 5d5dC 5d5eC C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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-Non-polymers , 5 types, 151 molecules
#2: Chemical | ChemComp-BR / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-ACY / | #5: Chemical | ChemComp-PE5 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.42 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.5-1 M NaBr, 50-100 mM CH3COONa, pH 4.5, and 15-30 %(v/v) PEG400 PH range: pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91881 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91881 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 35932 / % possible obs: 99.4 % / Redundancy: 11.2 % / Net I/σ(I): 6.39 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 0.97 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→35.057 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→35.057 Å
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Refine LS restraints |
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LS refinement shell |
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