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Yorodumi- PDB-1lod: INTERACTION OF A LEGUME LECTIN WITH TWO COMPONENTS OF THE BACTERI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lod | ||||||
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Title | INTERACTION OF A LEGUME LECTIN WITH TWO COMPONENTS OF THE BACTERIAL CELL WALL | ||||||
Components | (LEGUME ISOLECTIN I ...) x 2 | ||||||
Keywords | LECTIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lathyrus ochrus (yellow-flowered pea) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.05 Å | ||||||
Authors | Bourne, Y. / Cambillau, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1994 Title: Interaction of a legume lectin with two components of the bacterial cell wall. A crystallographic study. Authors: Bourne, Y. / Ayouba, A. / Rouge, P. / Cambillau, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lod.cif.gz | 193.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lod.ent.gz | 153.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lod_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1lod_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1lod_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 1lod_validation.cif.gz | 56.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/1lod ftp://data.pdbj.org/pub/pdb/validation_reports/lo/1lod | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Atom site foot note | 1: ALA A 80 - ASP A 81 OMEGA = 349.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: ALA C 80 - ASP C 81 OMEGA = 347.69 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: ALA E 80 - ASP E 81 OMEGA = 346.68 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 4: ALA G 80 - ASP G 81 OMEGA = 343.81 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Details | THIS CRYSTAL FORM CONTAINS TWO DIMERS IN THE ASYMMETRIC UNIT. EACH MONOMER CONSISTS OF TWO SEPARATE POLYPEPTIDE CHAINS, ALPHA AND BETA. THE ALPHA CHAIN CONSISTS OF 181 RESIDUES AND THE BETA CHAIN CONSISTS OF 52 RESIDUES. THE BETA AND ALPHA CHAINS OF MONOMER 1 HAVE BEEN ASSIGNED *A* AND *B*. THE BETA AND ALPHA CHAINS OF MONOMER 2 HAVE BEEN ASSIGNED *C* AND *D*. THE SAME ASSIGNMENT HAS BEEN MADE FOR THE SECOND MOLECULE WITH CHAIN IDENTIFIERS *E*, *F*, *G*, *H*. EACH DIMER HAS THE TWO MONOMERS WHICH ARE RELATED BY A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS. |
-Components
-LEGUME ISOLECTIN I ... , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 19847.857 Da / Num. of mol.: 4 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.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lathyrus ochrus (yellow-flowered pea) / Organ: SEED / References: UniProt: P12306 |
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-Sugars , 1 types, 4 molecules
#5: Sugar | ChemComp-MUR / |
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-Non-polymers , 3 types, 320 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MN / #6: Water | ChemComp-HOH / | |
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-Details
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: 2.41 Å3/Da / Density % sol: 48.98 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting dropDetails: Bourne, Y., (1990) Proteins Struct. Funct. Genet., 8, 365. | ||||||||||||||||||||||||||||||
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: 2.05 Å / Lowest resolution: 6 Å / Num. obs: 56334 / % possible obs: 95 % / Num. measured all: 224984 / Rmerge(I) obs: 0.073 |
-Processing
Software |
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Refinement | Resolution: 2.05→6 Å / Rfactor Rwork: 0.197 / Rfactor obs: 0.197 / σ(F): 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 55620 / Rfactor obs: 0.197 / Rfactor Rwork: 0.197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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