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Yorodumi- PDB-1loe: X-RAY CRYSTAL STRUCTURE DETERMINATION AND REFINEMENT AT 1.9 ANGST... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1loe | ||||||
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Title | X-RAY CRYSTAL STRUCTURE DETERMINATION AND REFINEMENT AT 1.9 ANGSTROMS RESOLUTION OF ISOLECTIN I FROM THE SEEDS OF LATHYRUS OCHRUS | ||||||
Components |
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Keywords | LECTIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lathyrus ochrus (yellow-flowered pea) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Bourne, Y. / Cambillau, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1990 Title: X-ray crystal structure determination and refinement at 1.9 A resolution of isolectin I from the seeds of Lathyrus ochrus. Authors: Bourne, Y. / Abergel, C. / Cambillau, C. / Frey, M. / Rouge, P. / Fontecilla-Camps, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1loe.cif.gz | 104 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1loe.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 1loe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1loe_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
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Full document | 1loe_full_validation.pdf.gz | 457.4 KB | Display | |
Data in XML | 1loe_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 1loe_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/1loe ftp://data.pdbj.org/pub/pdb/validation_reports/lo/1loe | 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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2 |
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3 |
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Unit cell |
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Atom site foot note | 1: ALA A 80 - ASP A 81 OMEGA =350.16 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: ALA C 80 - ASP C 81 OMEGA =339.46 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 19847.857 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lathyrus ochrus (yellow-flowered pea) / Organ: SEED / References: UniProt: P04122 #2: Protein | Mass: 5783.322 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lathyrus ochrus (yellow-flowered pea) / Organ: SEED / References: UniProt: P12306 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | THE AMINO-ACID SEQUENCE OF ISOLECTIN I SHOWS 85 PER CENT HOMOLOGY WITH THAT OF PEA LECTIN. | Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.05 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / 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 | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 9999 Å / Num. obs: 27484 / Observed criterion σ(I): 4.4 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2 Å / Num. unique obs: 2212 / Rmerge(I) obs: 0.255 |
-Processing
Software |
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Refinement | Resolution: 1.9→8 Å / Rfactor Rwork: 0.185 / Rfactor obs: 0.185 / σ(F): 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 25932 / Rfactor obs: 0.185 / Rfactor Rwork: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3 |