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Yorodumi- PDB-4prq: CRYSTAL STRUCTURE OF HEN EGG-WHITE LYSOZYME IN COMPLEX WITH SCLX4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4prq | ||||||
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Title | CRYSTAL STRUCTURE OF HEN EGG-WHITE LYSOZYME IN COMPLEX WITH SCLX4 AT 1.72 A RESOLUTION | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / HYDROLASE(O-GLYCOSYL) | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | McGovern, R.E. / McCarthy, A.A. / Crowley, P.B. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2014 Title: Protein assembly mediated by sulfonatocalix[4]arene. Authors: McGovern, R.E. / McCarthy, A.A. / Crowley, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4prq.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4prq.ent.gz | 100.5 KB | Display | PDB format |
PDBx/mmJSON format | 4prq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4prq_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 4prq_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4prq_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 4prq_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/4prq ftp://data.pdbj.org/pub/pdb/validation_reports/pr/4prq | HTTPS FTP |
-Related structure data
Related structure data | 2z12S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 4 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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-Non-polymers , 6 types, 337 molecules
#2: Chemical | ChemComp-T3Y / #3: Chemical | #4: Chemical | ChemComp-P6G / | #5: Chemical | ChemComp-PG6 / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.18 Å3/Da / Density % sol: 43.62 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 24 % PEG 8000, 100 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CHLORIDE, 50 MM SODIUM CACODYLATE, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.00792 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2012 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00792 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→42.47 Å / Num. all: 51816 / Num. obs: 51142 / % possible obs: 98.64 % / Redundancy: 3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.72→1.82 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 1.8 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2z12 Resolution: 1.72→42.47 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.772 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 22.815 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→42.47 Å
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Refine LS restraints |
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