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Yorodumi- PDB-1wtm: X-ray structure of HEW Lysozyme Orthorhombic Crystal formed in th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wtm | ||||||
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Title | X-ray structure of HEW Lysozyme Orthorhombic Crystal formed in the Earth's magnetic field | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Allergen | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | Saijo, S. / Yamada, Y. / Sato, T. / Tanaka, N. / Matsui, T. / Sazaki, G. / Nakajima, K. / Matsuura, Y. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structural consequences of hen egg-white lysozyme orthorhombic crystal growth in a high magnetic field: validation of X-ray diffraction intensity, conformational energy searching and ...Title: Structural consequences of hen egg-white lysozyme orthorhombic crystal growth in a high magnetic field: validation of X-ray diffraction intensity, conformational energy searching and quantitative analysis of B factors and mosaicity. Authors: Saijo, S. / Yamada, Y. / Sato, T. / Tanaka, N. / Matsui, T. / Sazaki, G. / Nakajima, K. / Matsuura, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wtm.cif.gz | 34.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wtm.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 1wtm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/1wtm ftp://data.pdbj.org/pub/pdb/validation_reports/wt/1wtm | 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) / Cell: egg / Cellular location: cytoplasm(white) / References: UniProt: P00698, lysozyme |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 8 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.52 % |
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Crystal grow | Temperature: 313 K / Method: in the earth's magnetic field / pH: 4.5 Details: NaCl, sodium acetate, pH 4.5, in the Earth's magnetic field, temperature 313K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.33→20 Å / Num. all: 21469 / Num. obs: 20095 / % possible obs: 93.6 % / Observed criterion σ(I): 3 | |||||||||||||||
Reflection shell | Resolution: 1.33→1.38 Å / % possible all: 62.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→16 Å / σ(F): 3
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Refine analyze | Luzzati coordinate error obs: 0.18 Å | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→16 Å
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Refine LS restraints |
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