+Open data
-Basic information
Entry | Database: PDB / ID: 1f0w | ||||||
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Title | CRYSTAL STRUCTURE OF ORTHORHOMBIC LYSOZYME GROWN AT PH 6.5 | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / ENZYME-ORTHORHOMBIC FORM / MUCOPEPTIDE N-ACETYLMURAMYL HYDROLASE / HEN EGG-WHITE LYSOZYME | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Biswal, B.K. / Sukumar, N. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Hydration, mobility and accessibility of lysozyme: structures of a pH 6.5 orthorhombic form and its low-humidity variant and a comparative study involving 20 crystallographically independent molecules. Authors: Biswal, B.K. / Sukumar, N. / Vijayan, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Protein Hydration and Water Structure: X-Ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content Authors: Madhusudan / Kodandapani, R. / Vijayan, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structures of Orthorhombic Lysozyme Grown at Basic pH and its Low-Humidity Variant Authors: Sukumar, N. / Biswal, B.K. / Vijayan, M. #3: Journal: J.Biol.Chem. / Year: 1990 Title: Crystal Structure of Low Humidity Tetragonal Lysozyme at 2.1-A Resolution. Variability in Hydration Shell and its Structural Consequences Authors: Kodandapani, R. / Suresh, C.G. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f0w.cif.gz | 35.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f0w.ent.gz | 27.9 KB | Display | PDB format |
PDBx/mmJSON format | 1f0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f0w_validation.pdf.gz | 410.3 KB | Display | wwPDB validaton report |
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Full document | 1f0w_full_validation.pdf.gz | 411.7 KB | Display | |
Data in XML | 1f0w_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1f0w_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/1f0w ftp://data.pdbj.org/pub/pdb/validation_reports/f0/1f0w | HTTPS FTP |
-Related 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 / Details: CRYSTAL STRUCTURE OF ORTHORHOMBIC FORM / Source: (natural) Gallus gallus (chicken) / Cellular location: CYTOPLASM / Tissue fraction: EGG WHITE / 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: 2.17 Å3/Da / Density % sol: 43.34 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 42.2 % | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Detector: IMAGE PLATE | ||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection | Resolution: 1.9→27.4 Å / Num. obs: 10122 / % possible obs: 97.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18 | ||||||||||||||||||||
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 1.6 / % possible all: 94.7 | ||||||||||||||||||||
Reflection | *PLUS Num. measured all: 42921 | ||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 94.7 % / Num. unique obs: 1351 |
-Processing
Software |
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Refinement | Resolution: 1.9→10 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 24.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.085 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.489 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.363 |