+Open data
-Basic information
Entry | Database: PDB / ID: 3wpk | ||||||
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Title | SPATIOTEMPORAL DEVELOPMENT of SOAKED PROTEIN CRYSTAL; 750 SEC | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / BACTERIAL CELL WALL LYSIS | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Mizutani, R. / Saiga, R. | ||||||
Citation | Journal: Sci Rep / Year: 2014 Title: Spatiotemporal development of soaked protein crystal Authors: Mizutani, R. / Shimizu, Y. / Saiga, R. / Ueno, G. / Nakamura, Y. / Takeuchi, A. / Uesugi, K. / Suzuki, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wpk.cif.gz | 39.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wpk.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 3wpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wpk_validation.pdf.gz | 412 KB | Display | wwPDB validaton report |
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Full document | 3wpk_full_validation.pdf.gz | 412 KB | Display | |
Data in XML | 3wpk_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 3wpk_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/3wpk ftp://data.pdbj.org/pub/pdb/validation_reports/wp/3wpk | HTTPS FTP |
-Related structure data
Related structure data | 3wpjC 3wplC 3wu7C 3wu8C 3wu9C 3wuaC 2lymS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | THE ORIGINAL NUMBERs OF HOHs HAVE BEEN RENUMBERED. ORIGINAL RENUMBERED HOH(130, CHAIN A) HOH(401, ...THE ORIGINAL NUMBERs OF HOHs HAVE BEEN RENUMBERED | |
-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: 40.62 % |
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Crystal grow | Temperature: 293 K / Method: batch method / pH: 4.5 Details: 25mg/ml Lysozyme, 0.05M SODIUM ACETATE, 0.7M SODIUM CHLORIDE, pH 4.5, BATCH METHOD, temperature 293K |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1.07345 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2013 |
Radiation | Monochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07345 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 8615 / Num. obs: 8581 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rsym value: 0.079 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 7 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 412 / Rsym value: 0.238 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2LYM Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.566 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 19.322 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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