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Yorodumi- PDB-1len: REFINEMENT OF TWO CRYSTAL FORMS OF LENTIL LECTIN AT 1.8 ANGSTROMS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1len | ||||||
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Title | REFINEMENT OF TWO CRYSTAL FORMS OF LENTIL LECTIN AT 1.8 ANGSTROMS RESOLUTION | ||||||
Components | (LECTIN) x 2 | ||||||
Keywords | LECTIN | ||||||
Function / homology | Function and homology information carbohydrate mediated signaling / D-mannose binding / manganese ion binding / carbohydrate binding / calcium ion binding Similarity search - Function | ||||||
Biological species | Lens culinaris (lentil) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Van Overberge, D. / Loris, R. / Wyns, L. | ||||||
Citation | Journal: Proteins / Year: 1994 Title: Structural analysis of two crystal forms of lentil lectin at 1.8 A resolution. Authors: Loris, R. / Van Overberge, D. / Dao-Thi, M.H. / Poortmans, F. / Maene, N. / Wyns, L. #1: Journal: Biochemistry / Year: 1993 Title: Crystal Structure Determination and Refinement at 2.3 Angstroms Resolution of the Lentil Lectin Authors: Loris, R. / Steyaert, J. / Maes, D. / Lisgarten, J. / Pickersgill, R. / Wyns, L. #2: Journal: J.Mol.Biol. / Year: 1992 Title: Two Crystal Forms of the Lentil Lectin Diffract to High Resolution Authors: Loris, R. / Lisgarten, J. / Maes, D. / Pickersgill, R. / Korber, F. / Reynolds, C. / Wyns, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1len.cif.gz | 105.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1len.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 1len.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/1len ftp://data.pdbj.org/pub/pdb/validation_reports/le/1len | 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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Atom site foot note | 1: ALA A 80 - ASP A 81 OMEGA =356.62 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: ALA C 80 - ASP C 81 OMEGA =358.29 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 19906.982 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lens culinaris (lentil) / References: UniProt: P02870 #2: Protein | Mass: 5714.288 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lens culinaris (lentil) / References: UniProt: P02870 |
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-Non-polymers , 4 types, 237 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | EACH MONOMER HAS A BOUND CALCIUM, MANGANESE AMD PHOSPHATE ION. THE CALCIUM AND MANGANESE IONS ARE ...EACH MONOMER HAS A BOUND CALCIUM, MANGANESE AMD PHOSPHATE ION. THE CALCIUM AND MANGANESE IONS ARE ESSENTIAL FOR STABILIZIN |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.27 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: batch method | ||||||||||||||||||||||||||||||
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 | *PLUS Highest resolution: 1.75 Å / Num. obs: 53882 / % possible obs: 83.7 % / Num. measured all: 169906 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 74.2 % / Rmerge(I) obs: 0.269 |
-Processing
Software | Name: RESTRAIN / Classification: refinement | |||||||||||||||||||||
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Refinement | Rfactor obs: 0.175 / Highest resolution: 1.8 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.175 / Rfactor Rwork: 0.175 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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