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Yorodumi- PDB-1rin: X-RAY CRYSTAL STRUCTURE OF A PEA LECTIN-TRIMANNOSIDE COMPLEX AT 2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rin | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF A PEA LECTIN-TRIMANNOSIDE COMPLEX AT 2.6 ANGSTROMS RESOLUTION | ||||||
Components | (PEA LECTIN) x 2 | ||||||
Keywords | LECTIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pisum sativum (garden pea) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Rini, J.M. / Hardman, K.D. / Einspahr, H. / Suddath, F.L. / Carver, J.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1993 Title: X-ray crystal structure of a pea lectin-trimannoside complex at 2.6 A resolution. Authors: Rini, J.M. / Hardman, K.D. / Einspahr, H. / Suddath, F.L. / Carver, J.P. #1: Journal: J.Mol.Biol. / Year: 1986 Title: Crystallization and Preliminary X-Ray Diffraction Studies of a Pea Lectin-Methyl 3,6-Di-O(Alpha-D-Mannopyranosyl)-Alpha-D-Mannopyranoside Complex Authors: Rini, J.M. / Carver, J.P. / Hardman, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rin.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rin.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 1rin.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rin_validation.pdf.gz | 405.7 KB | Display | wwPDB validaton report |
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Full document | 1rin_full_validation.pdf.gz | 413.9 KB | Display | |
Data in XML | 1rin_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1rin_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/1rin ftp://data.pdbj.org/pub/pdb/validation_reports/ri/1rin | 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: THE PEPTIDE BONDS ALA A 80 - ASP A 81 AND ALA C 80 -ASP C 81 ARE IN THE CIS CONFORMATION. THIS FEATURE IS COMMON TO THIS FAMILY OF LECTINS. |
-Components
-Protein / Protein/peptide / Sugars , 3 types, 6 molecules ACBD
#1: Protein | Mass: 19887.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / References: UniProt: P02867 #2: Protein/peptide | Mass: 5334.854 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / References: UniProt: P02867 #3: Sugar | |
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-Non-polymers , 3 types, 91 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | ELECTRON DENSITY FOR ONE TERMINAL MANNOSE RESIDUE OF THE TRISACCHARIDE IS SEEN IN EACH OF THE ...ELECTRON DENSITY FOR ONE TERMINAL MANNOSE RESIDUE OF THE TRISACCHAR |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.52 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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: 2.5 Å / Num. obs: 17124 / Rmerge(I) obs: 0.076 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.183 / Rfactor obs: 0.183 / Highest resolution: 2.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.9 |