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Open data
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Basic information
Entry | Database: PDB / ID: 1qdd | |||||||||
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Title | CRYSTAL STRUCTURE OF HUMAN LITHOSTATHINE TO 1.3 A RESOLUTION | |||||||||
![]() | LITHOSTATHINE | |||||||||
![]() | METAL BINDING PROTEIN / Pancreatic Stone Inhibitor / Lithostathine | |||||||||
Function / homology | ![]() 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 / collagen-containing extracellular matrix / positive regulation of cell population proliferation ...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 / collagen-containing extracellular matrix / positive regulation of cell population proliferation / extracellular space / extracellular exosome Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Gerbaud, V. / Pignol, D. / Loret, E. / Bertrand, J.A. / Berland, Y. / Fontecilla-Camps, J.C. / Canselier, J.P. / Gabas, N. / Verdier, J.M. | |||||||||
![]() | ![]() Title: Mechanism of calcite crystal growth inhibition by the N-terminal undecapeptide of lithostathine. Authors: Gerbaud, V. / Pignol, D. / Loret, E. / Bertrand, J.A. / Berland, Y. / Fontecilla-Camps, J.C. / Canselier, J.P. / Gabas, N. / Verdier, J.M. #1: ![]() Title: Crystal structure of human lithostathine, the pancreatic inhibitor of stone formation Authors: Bertrand, J. / Pignol, D. / Bernard, J.P. / Verdier, J.M. / Dagorn, J.C. / Fontecilla-Camps, J.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.5 KB | Display | ![]() |
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PDB format | ![]() | 32.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457 KB | Display | ![]() |
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Full document | ![]() | 460.3 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Data in CIF | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 16204.920 Da / Num. of mol.: 1 / Mutation: ALA88ARG / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Polysaccharide | beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.98 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: PEG 4000, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃Details: Pignol, D., (1995) Proteins: Struct.,Funct., Genet., 23, 604. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→20 Å / Num. all: 32253 / Num. obs: 32253 / % possible obs: 95.4 % / Rmerge(I) obs: 0.084 |
Reflection shell | Highest resolution: 1.3 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.28 / % possible all: 96.2 |
Reflection | *PLUS Num. measured all: 114712 |
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Processing
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Refinement | Resolution: 1.3→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / Rfactor Rwork: 0.132 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS |