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Yorodumi- PDB-2nwd: Structure of chemically synthesized human lysozyme at 1 Angstrom ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nwd | ||||||
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Title | Structure of chemically synthesized human lysozyme at 1 Angstrom resolution | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / native chemical ligation / chemical protein synthesis / convergent synthesis | ||||||
Function / homology | Function and homology information antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | ||||||
Authors | Durek, T. / Torbeev, V.Y. / Kent, S.B.H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Convergent chemical synthesis and high-resolution x-ray structure of human lysozyme. Authors: Durek, T. / Torbeev, V.Y. / Kent, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nwd.cif.gz | 124.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nwd.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 2nwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/2nwd ftp://data.pdbj.org/pub/pdb/validation_reports/nw/2nwd | HTTPS FTP |
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-Related structure data
Related structure data | 1jsfS 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
#1: Protein | Mass: 14720.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical Protein Synthesis / References: UniProt: P61626, 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: 1.92 Å3/Da / Density % sol: 35.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: c 6 mg/mL, 60 mM LiCl, 1.25 mM Hepes, 15 mM sodium phosphate, 1.25 M NaCl , pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→50 Å / Num. obs: 53675 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JSF, see ref. K. Harada, Y. abe, M. Muraki, Proteins, 1998, 30, 232. Resolution: 1.04→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.651 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.171 Å2
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Refinement step | Cycle: LAST / Resolution: 1.04→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.041→1.068 Å / Total num. of bins used: 20
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