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Yorodumi- PDB-3agi: High resolution X-ray analysis of Arg-lysozyme complex in the pre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3agi | ||||||
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Title | High resolution X-ray analysis of Arg-lysozyme complex in the presence of 500 mM Arg | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / lysozyme / glycosidase / arginine / Allergen / Antimicrobial / Bacteriolytic enzyme / Disulfide bond | ||||||
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: 1.2 Å | ||||||
Authors | Ito, L. / Shiraki, K. / Hasegawa, K. / Baba, S. / Kumasaka, T. | ||||||
Citation | Journal: Protein Eng.Des.Sel. / Year: 2011 Title: High-resolution X-ray analysis reveals binding of arginine to aromatic residues of lysozyme surface: implication of suppression of protein aggregation by arginine Authors: Ito, L. / Shiraki, K. / Matsuura, T. / Okumura, M. / Hasegawa, K. / Baba, S. / Yamaguchi, H. / Kumasaka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3agi.cif.gz | 78.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3agi.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 3agi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3agi_validation.pdf.gz | 457 KB | Display | wwPDB validaton report |
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Full document | 3agi_full_validation.pdf.gz | 459.1 KB | Display | |
Data in XML | 3agi_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 3agi_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/3agi ftp://data.pdbj.org/pub/pdb/validation_reports/ag/3agi | HTTPS FTP |
-Related structure data
Related structure data | 3aggC 3aghC 3a34S S: Starting model for refinement 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: commercially available / Source: (natural) Gallus gallus (chicken) / Tissue: egg / References: UniProt: P00698, lysozyme |
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-Non-polymers , 5 types, 196 molecules
#2: Chemical | ChemComp-ACT / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-CL / #6: 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: 2.01 Å3/Da / Density % sol: 38.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.5 Details: 0.05 M Sodium Acetate 1.6 M Sodium Chloride 0.5 M Arg, pH 4.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 34994 / Redundancy: 14.7 % / Rmerge(I) obs: 0.052 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.3 / Num. unique all: 6969 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3A34 Resolution: 1.2→39.02 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.894 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.039 / 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: 14.183 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→39.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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