+Open data
-Basic information
Entry | Database: PDB / ID: 1lks | ||||||
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Title | HEN EGG WHITE LYSOZYME NITRATE | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / LYSOZYME | ||||||
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 / Resolution: 1.1 Å | ||||||
Authors | Steinrauf, L.K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Structures of monoclinic lysozyme iodide at 1.6 A and of triclinic lysozyme nitrate at 1.1 A. Authors: Steinrauf, L.K. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Studies of Monoclinic Hen Egg-White Lysozyme. Iv. X-Ray Refinement at 1.8 A Resolution and a Comparison of the Variable Regions in the Polymorphic Forms Authors: Rao, S.T. / Sundaralingam, M. #2: Journal: Acta Crystallogr.,Sect.C / Year: 1983 Title: Studies of Monoclinic Hen Egg White Lysozyme. II. The Refinement at 2.5 A Resolution--Conformational Variability between the Two Independent Molecules Authors: Rao, S.T. / Hogle, J. / Sundaralingam, M. #3: Journal: Acta Crystallogr. / Year: 1959 Title: Preliminary X-Ray Data for Some New Crystalline Forms of Beta-Lactoglobulin and Hen Egg-White Lysozyme Authors: Steinrauf, L.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lks.cif.gz | 70.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lks.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/1lks ftp://data.pdbj.org/pub/pdb/validation_reports/lk/1lks | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||
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#2: Chemical | ChemComp-NO3 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 26 % | ||||||||||||||||||||
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Crystal grow | Details: THE CRYSTALS WERE GROWN IN THE PRESENCE OF BROMO PHENYL BLUE (BPB), AND THE CRYSTALS WERE DARK BLUE, ALMOST BLACK. HOWEVER, NO RELIABLE TRACE OF THE BPB WAS FOUND. | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS pH: 4.7 / Method: batch method | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 15, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→20 Å / Num. obs: 36397 / % possible obs: 78.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.095 |
Reflection | *PLUS Num. measured all: 216397 |
-Processing
Software |
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Refinement | Resolution: 1.1→20 Å / Cross valid method: FREE R / σ(F): 1 Details: WATER MOLECULES 272, 333, AND 319, HAVE NO REASONABLE PROTEIN CONTACTS AND MAY BE PART OF THE UNRESOLVED BROMO PHENOL BLUE DISORDER.
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Refinement step | Cycle: LAST / Resolution: 1.1→20 Å
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Software | *PLUS Name: SHELXL-93 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.1101 / Rfactor obs: 0.0989 / Rfactor Rfree: 0.1416 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS |