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Yorodumi- PDB-1f10: CRYSTAL STRUCTURE OF ORTHORHOMBIC LYSOZYME GROWN AT PH 6.5 AT 88%... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f10 | ||||||
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Title | CRYSTAL STRUCTURE OF ORTHORHOMBIC LYSOZYME GROWN AT PH 6.5 AT 88% RELATIVE HUMIDITY | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / ENZYME-ORTHORHOMBIC FORM / MUCOPEPTIDE N-ACETYLMURAMYL HYDROLASE / HEN EGG-WHITE LYSOZYME / LOW HUMIDITY | ||||||
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: 1.7 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 | 1f10.cif.gz | 39.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f10.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 1f10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/1f10 ftp://data.pdbj.org/pub/pdb/validation_reports/f1/1f10 | 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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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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: 2.04 Å3/Da / Density % sol: 39.81 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 38.5 % | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
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: 1.7→25 Å / Num. obs: 13459 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.7→1.8 Å / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 54245 |
Reflection shell | *PLUS Num. unique obs: 2083 |
-Processing
Software |
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Refinement | Starting model: ORTHORHOMBIC LYSOZYME AT PH 6.5 Resolution: 1.7→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 20.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.046 / 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: 20.8 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.486 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.414 |