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Yorodumi- PDB-1loc: INTERACTION OF A LEGUME LECTIN WITH TWO COMPONENTS OF THE BACTERI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1loc | ||||||||||||
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Title | INTERACTION OF A LEGUME LECTIN WITH TWO COMPONENTS OF THE BACTERIAL CELL WALL | ||||||||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / LECTIN | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Lathyrus ochrus (yellow-flowered pea) synthetic construct (others) | ||||||||||||
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 | 1loc.cif.gz | 196.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1loc.ent.gz | 156 KB | Display | PDB format |
PDBx/mmJSON format | 1loc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1loc_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1loc_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1loc_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 1loc_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/1loc ftp://data.pdbj.org/pub/pdb/validation_reports/lo/1loc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: ALA A 80 - ASP A 81 OMEGA = 347.11 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: ALA C 80 - ASP C 81 OMEGA = 347.61 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: ALA E 80 - ASP E 81 OMEGA = 342.86 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 4: ALA G 80 - ASP G 81 OMEGA = 346.01 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, ONE CA++ AND ONE MN++ ION, AND THE MURAMYL-DIPEPTIDE. THE ALPHA CHAIN CONSISTS OF 181 RESIDUES AND THE BETA CHAIN CONSISTS OF 52 RESIDUES. MONOMER 1 CONTAINS ALPHA CHAIN *A*, BETA CHAIN *B*, MURAMYL-DIPEPTIDE *1*, CA 228, AND MN 229. MONOMER 2 CONTAINS ALPHA CHAIN *C*, BETA CHAIN *D* AND MURAMYL- DIPEPTIDE *2*. MONOMERS 3 AND 4 ARE LABELLED SIMILARLY, WITH CHAIN IDENTIFIERS *E*, *F*, *3*, *G*, *H* AND *4*. EACH DIMER HAS 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 natural source / Source: (natural) 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 natural source / Source: (natural) Lathyrus ochrus (yellow-flowered pea) / Organ: SEED / References: UniProt: P12306 |
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-Protein/peptide / Sugars , 2 types, 8 molecules 1234
#3: Protein/peptide | Mass: 217.222 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #6: Sugar | ChemComp-MDP / |
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-Non-polymers , 3 types, 326 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-MN / #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE MURAMYL-DIPEPTIDE D-ALA-D-IGLN OCCURS 4 TIMES, ONCE IN EACH MONOMER. IT IS REPRESENTED AS MDP- ...THE MURAMYL-DIPEPTIDE D-ALA-D-IGLN OCCURS 4 TIMES, ONCE IN EACH MONOMER. IT IS REPRESENTE |
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Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.68 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting dropDetails: reservoirs contain the same ingredients as drops, but twice as consentrated. taken from Bourne, Y. et al. (1988). J. Mol. Biol., 202, 685-687. | ||||||||||||||||||||||||||||||
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: 57554 / % possible obs: 97 % / Num. measured all: 248619 / Rmerge(I) obs: 0.069 |
-Processing
Software |
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Refinement | Resolution: 2.05→6 Å / Rfactor Rwork: 0.189 / Rfactor obs: 0.189 / 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: 57175 / Rfactor obs: 0.189 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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