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Yorodumi- PDB-4nhi: Crystal structure of Hen egg-white lysozyme in Tris buffer at pH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nhi | ||||||
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Title | Crystal structure of Hen egg-white lysozyme in Tris buffer at pH 7.5 with Magnesium formate | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / catalytic activity / protein binding / acting on glycosyl bonds / identical protein binding / extracellular region | ||||||
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: 1.34 Å | ||||||
Authors | Lim, H. / Rho, J. / Hyun, J.K. / Kim, Y.J. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Hen egg-white lysozyme in Tris buffer at pH 7.5 with Magnesium formate Authors: Lim, H. / Rho, J. / Hyun, J.K. / Kim, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nhi.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nhi.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 4nhi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/4nhi ftp://data.pdbj.org/pub/pdb/validation_reports/nh/4nhi | HTTPS FTP |
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-Related structure data
Related structure data | 2lyzS 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 Details: Lysozyme from chicken egg white ,62971 FLUKA, powder (crystalline), white, ~70000 U/mg Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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#2: 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: 1.9 Å3/Da / Density % sol: 35.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 80mg/ml hen egg-white lysozyme, 100mM TrisHCl, 0.4M Mg-Formate(0.2~0.6 M), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 23, 2013 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.34→50 Å / Num. all: 349012 / Num. obs: 349012 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 59.724 |
Reflection shell | Resolution: 1.34→1.36 Å / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.536 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LYZ Resolution: 1.34→38.3 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.271 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R Free: 0.014 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.282 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→38.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.338→1.372 Å / Total num. of bins used: 20
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