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Yorodumi- PDB-1lmt: STRUCTURE OF A CONFORMATIONALLY CONSTRAINED ARG-GLY-ASP SEQUENCE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lmt | |||||||||
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Title | STRUCTURE OF A CONFORMATIONALLY CONSTRAINED ARG-GLY-ASP SEQUENCE INSERTED INTO HUMAN LYSOZYME | |||||||||
Components | HUMAN LYSOZYME | |||||||||
Keywords | HYDROLASE (O-GLYCOSYL) | |||||||||
Function / homology | Function and homology information cytolysis / antimicrobial humoral response / retina homeostasis / metabolic process / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity ...cytolysis / antimicrobial humoral response / retina homeostasis / metabolic process / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.6 Å | |||||||||
Authors | Matsushima, M. / Song, H. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1995 Title: Structure of a conformationally constrained Arg-Gly-Asp sequence inserted into human lysozyme. Authors: Yamada, T. / Song, H. / Inaka, K. / Shimada, Y. / Kikuchi, M. / Matsushima, M. #1: Journal: J.Biol.Chem. / Year: 1993 Title: Structural and Functional Analyses of the Arg-Gly-Asp Sequence Introduced Into Human Lysozyme Authors: Yamada, T. / Matsushima, M. / Inaka, K. / Ohkubo, T. / Uyeda, A. / Maeda, T. / Titani, K. / Sekiguchi, K. / Kikuchi, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lmt.cif.gz | 39.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lmt.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lmt_validation.pdf.gz | 763.2 KB | Display | wwPDB validaton report |
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Full document | 1lmt_full_validation.pdf.gz | 766.2 KB | Display | |
Data in XML | 1lmt_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1lmt_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/1lmt ftp://data.pdbj.org/pub/pdb/validation_reports/lm/1lmt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15343.392 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00695, UniProt: P61626*PLUS, lysozyme | ||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | THE LYSOZYME MOLECULE BINDS THE SACCHARIDE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.93 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 13.0 ℃ / pH: 6 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.6→6 Å |
Reflection | *PLUS Num. obs: 12925 / Rmerge(I) obs: 0.051 |
-Processing
Software |
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Refinement | Highest resolution: 1.6 Å /
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Refinement step | Cycle: LAST / Highest resolution: 1.6 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 0.034 |