+Open data
-Basic information
Entry | Database: PDB / ID: 1lit | ||||||
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Title | HUMAN LITHOSTATHINE | ||||||
Components | LITHOSTATHINE | ||||||
Keywords | PANCREATIC STONE INHIBITOR / LECTIN | ||||||
Function / homology | Function and homology information disruption of cell wall in another organism / oligosaccharide binding / peptidoglycan binding / molecular function inhibitor activity / growth factor activity / response to peptide hormone / antimicrobial humoral immune response mediated by antimicrobial peptide / signaling receptor activity / positive regulation of cell population proliferation / extracellular space / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å | ||||||
Authors | Bertrand, J.A. / Pignol, D. / Bernard, J.-P. / Verdier, J.-M. / Dagorn, J.-C. / Fontacilla-Camps, J.C. | ||||||
Citation | Journal: EMBO J. / Year: 1996 Title: Crystal structure of human lithostathine, the pancreatic inhibitor of stone formation. Authors: Bertrand, J.A. / Pignol, D. / Bernard, J.P. / Verdier, J.M. / Dagorn, J.C. / Fontecilla-Camps, J.C. #1: Journal: Proteins / Year: 1995 Title: Crystallization and Preliminary Crystallographic Study of Human Lithostathine Authors: Pignol, D. / Bertrand, J.A. / Bernard, J.P. / Verdier, J.M. / Dagorn, J.C. / Fontacilla-Camps, J.C. #2: Journal: Gastroenterology / Year: 1992 Title: Inhibition of Nucleation and Crystal Growth of Calcium Carbonate Crystals by Human Lithostathine Authors: Bernard, J.P. / Adrich, Z. / Montalto, G. / Decaro, A. / De Reggi, M. / Sarles, H. / Dagorn, J-C. #3: Journal: Biochem.J. / Year: 1988 Title: Homology of Human Pancreatic Stone Protein with Animal Lectins Authors: Patthy, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lit.cif.gz | 37.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lit.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/1lit ftp://data.pdbj.org/pub/pdb/validation_reports/li/1lit | HTTPS FTP |
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-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: 16291.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PANCREAS / References: UniProt: P05451 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging dropDetails: Pignol, D., (1995) Proteins: Struct.,Funct., Genet., 23, 604. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Num. obs: 19356 / % possible obs: 98.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.042 |
-Processing
Software |
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Refinement | Resolution: 1.55→8 Å
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Displacement parameters | Biso mean: 23.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 19532 / Rfactor obs: 0.186 / Rfactor Rfree: 0.244 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.01 |