+Open data
-Basic information
Entry | Database: PDB / ID: 1dyk | ||||||
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Title | Laminin alpha 2 chain LG4-5 domain pair | ||||||
Components | LAMININ ALPHA 2 CHAIN | ||||||
Keywords | METAL BINDING PROTEIN / LAMININ | ||||||
Function / homology | Function and homology information regulation of basement membrane organization / Schwann cell differentiation / positive regulation of synaptic transmission, cholinergic / positive regulation of integrin-mediated signaling pathway / tissue development / protein complex involved in cell-matrix adhesion / extracellular matrix structural constituent / positive regulation of muscle cell differentiation / regulation of embryonic development / positive regulation of cell adhesion ...regulation of basement membrane organization / Schwann cell differentiation / positive regulation of synaptic transmission, cholinergic / positive regulation of integrin-mediated signaling pathway / tissue development / protein complex involved in cell-matrix adhesion / extracellular matrix structural constituent / positive regulation of muscle cell differentiation / regulation of embryonic development / positive regulation of cell adhesion / basement membrane / synaptic cleft / regulation of cell migration / axon guidance / animal organ morphogenesis / neuromuscular junction / sarcolemma / collagen-containing extracellular matrix / dendritic spine / cell adhesion / signaling receptor binding / extracellular region Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Tisi, D. / Talts, J.F. / Timple, R. / Hohenester, E. | ||||||
Citation | Journal: Embo J. / Year: 2000 Title: Structure of the C-Terminal Laminin G-Like Domain Pair of the Laminin Alpha 2 Chain Harbouring Binding Sites for Alpha-Dystroglycan and Heparin Authors: Tisi, D. / Talts, J.F. / Timpl, R. / Hohenester, E. #1: Journal: Mol.Cell / Year: 1999 Title: The Crystal Structure of a Laminin G-Like Module Reveals the Molecular Basis of Alpha-Dystroglycan Binding to Laminins, Perlecan and Agrin Authors: Hohenester, E. / Tisi, D. / Talts, J.F. / Timpl, R. #2: Journal: FEBS Lett. / Year: 1998 Title: Structural Analysis and Proteolytic Processing of Recombinant G Domain of Mouse Laminin Alpha 2 Chain Authors: Talts, J.F. / Mann, K. / Yamada, Y. / Timpl, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dyk.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dyk.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 1dyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dyk_validation.pdf.gz | 429 KB | Display | wwPDB validaton report |
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Full document | 1dyk_full_validation.pdf.gz | 433.7 KB | Display | |
Data in XML | 1dyk_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 1dyk_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/1dyk ftp://data.pdbj.org/pub/pdb/validation_reports/dy/1dyk | HTTPS FTP |
-Related structure data
Related structure data | 1qu0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42743.570 Da / Num. of mol.: 1 / Fragment: LAMININ G-LIKE DOMAIN 4-5 PAIR / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: FVB/N / Tissue: EMBRYO / Plasmid: PCEP-PU / Cell (production host): EMRYONIC KIDNEY CELL / Cell line (production host): EBNA-293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q60675 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE SWISSPROT SEQUENCE IS TAKEN FROM BERNIER S.M., UTANI A., SUGIYAMA S., DOI T., POLISTINA C., ...THE SWISSPROT SEQUENCE IS TAKEN FROM BERNIER S.M., UTANI A., SUGIYAMA S., DOI T., POLISTINA C., YAMADA Y. MATRIX BIOL. 14:447-455(1995). THE 21 RESIDUES OF THE C-TERMINUS DO NOT MATCH WITH THE SEQUENCE DATABASE REFERENCE PROVIDED. THE COORDINATE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.19 % Description: MOLECULAR REPLACEMENT PLUS SIR FROM SM DERIVATIVE | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC QUANTUM 4 CCD / Detector: CCD / Date: Oct 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 31704 / % possible obs: 94.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.139 / % possible all: 93.6 |
Reflection shell | *PLUS % possible obs: 93.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QU0 Resolution: 2→20 Å / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection Rfree: 2244 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |