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Yorodumi- PDB-2lal: CRYSTAL STRUCTURE DETERMINATION AND REFINEMENT AT 2.3 ANGSTROMS R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lal | ||||||
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Title | CRYSTAL STRUCTURE DETERMINATION AND REFINEMENT AT 2.3 ANGSTROMS RESOLUTION OF THE LENTIL LECTIN | ||||||
Components | (LENTIL 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 | Loris, R. / Steyaert, J. / Maes, D. / Lisgarten, J. / Pickersgill, 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: 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 | 2lal.cif.gz | 103.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lal.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 2lal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lal_validation.pdf.gz | 411.8 KB | Display | wwPDB validaton report |
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Full document | 2lal_full_validation.pdf.gz | 442 KB | Display | |
Data in XML | 2lal_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 2lal_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/2lal ftp://data.pdbj.org/pub/pdb/validation_reports/la/2lal | HTTPS FTP |
-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: THE PEPTIDE BOND BETWEEN ALA A 80 AND ASP A 81 AND THE PEPTIDE BOND BETWEEN ALA C 80 AND ASP C 81 ARE BOTH IN THE CIS CONFORMATION. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.999971, 0.004373, -0.006242), Vector: |
-Components
-LENTIL LECTIN ... , 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) / Organ: SEED / 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) / Organ: SEED / References: UniProt: P02870 |
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-Non-polymers , 4 types, 221 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound 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: 2.62 Å3/Da / Density % sol: 53.07 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: batch method | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 39656 / % possible obs: 75.5 % / Num. measured all: 108765 / Rmerge(I) obs: 0.056 |
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Reflection shell | *PLUS % possible obs: 63.1 % / Rmerge(I) obs: 0.238 |
-Processing
Software | Name: RESTRAIN / Classification: refinement | ||||||||||||
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Refinement | Rfactor obs: 0.189 / 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 Highest resolution: 1.8 Å / Rfactor obs: 0.184 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS Type: p_plane_restr / Dev ideal: 0.013 |