+Open data
-Basic information
Entry | Database: PDB / ID: 1azf | ||||||
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Title | CHICKEN EGG WHITE LYSOZYME CRYSTAL GROWN IN BROMIDE SOLUTION | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / O-GLYCOSYL HYDROLASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Lim, K. / Nadarajah, A. / Forsythe, E.L. / Pusey, M.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Locations of bromide ions in tetragonal lysozyme crystals. Authors: Lim, K. / Nadarajah, A. / Forsythe, E.L. / Pusey, M.L. #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.D / Year: 1996 Title: High-Resolution Structure (1.33 A) of a Hew Lysozyme Tetragonal Crystal Grown in the Apcf Apparatus. Data and Structural Comparison with a Crystal Grown Under Microgravity from Spacehab-01 Mission Authors: Vaney, M.C. / Maignan, S. / Ries-Kautt, M. / Ducruix, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1azf.cif.gz | 34.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1azf.ent.gz | 25.9 KB | Display | PDB format |
PDBx/mmJSON format | 1azf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1azf_validation.pdf.gz | 418.3 KB | Display | wwPDB validaton report |
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Full document | 1azf_full_validation.pdf.gz | 419 KB | Display | |
Data in XML | 1azf_validation.xml.gz | 8 KB | Display | |
Data in CIF | 1azf_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/1azf ftp://data.pdbj.org/pub/pdb/validation_reports/az/1azf | HTTPS FTP |
-Related structure data
Related structure data | 6lyzS 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: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM (WHITE) / References: UniProt: P00698, lysozyme | ||||
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#2: Chemical | ChemComp-BR / #3: Water | ChemComp-HOH / | Nonpolymer details | HOH 212 IS A POSSIBLE FIFTH BROMIDE POSITION. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.77 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.6 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→55.85 Å / Num. obs: 14036 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.65→2 Å / Rmerge(I) obs: 0.203 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 6LYZ Resolution: 1.8→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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