+Open data
-Basic information
Entry | Database: PDB / ID: 1hsx | ||||||
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Title | LYSOZYME GROWN AT BASIC PH AND ITS LOW HUMIDITY VARIANT | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / ENZYME-ORTHORHOMBIC FORM | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sukumar, N. / Biswal, B.K. / Vijayan, M. | ||||||
Citation | 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. #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.B / Year: 1990 Title: Refinement of Triclinic Lysozyme. II. The Method of Stereochemically Restrained Least-Squares Authors: Ramanadham, M. / Sieker, L.C. / Jensen, L.H. #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. #4: Journal: Acta Crystallogr.,Sect.B / Year: 1982 Title: The Structures of the Monoclinic and Orthorhombic Forms of Hen Egg-White Lysozyme at 6 Angstroms Resolution Authors: Artymiuk, P.J. / Blake, C.C.F. / Rice, D.W. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hsx.cif.gz | 40.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hsx.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 1hsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/1hsx ftp://data.pdbj.org/pub/pdb/validation_reports/hs/1hsx | 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 / Details: CRYSTAL STRUCTURE OF ORTHORHOMBIC FORM / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM (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: 2.18 Å3/Da / Density % sol: 43 % | |||||||||||||||||||||
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Crystal grow | pH: 9.6 / Details: pH 9.6 | |||||||||||||||||||||
Crystal | *PLUS Density % sol: 43 % | |||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / pH: 9.3 | |||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Detector: IMAGE PLATE / Date: Jun 3, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 10287 / % possible obs: 99.3 % / Redundancy: 7.08 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.0989 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 4.8 |
Reflection | *PLUS Num. measured all: 72266 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NATIVE TETRAGONAL FORM Resolution: 1.9→10 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 23.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.054 / Total num. of bins used: 6
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.33 |