+Open data
-Basic information
Entry | Database: PDB / ID: 1okq | ||||||
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Title | LAMININ ALPHA 2 CHAIN LG4-5 DOMAIN PAIR, CA1 SITE MUTANT | ||||||
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 / basement membrane ...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 / basement membrane / positive regulation of cell adhesion / synaptic cleft / regulation of cell migration / axon guidance / animal organ morphogenesis / sarcolemma / neuromuscular junction / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Wizemann, H. / Garbe, J.H.O. / Friedrich, M.V.K. / Timpl, R. / Sasaki, T. / Hohenester, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Distinct Requirements for Heparin and Alpha-Dystroglycan Binding Revealed by Structure-Based Mutagenesis of the Laminin Alpha2 Lg4-Lg5 Domain Pair Authors: Wizemann, H. / Garbe, J.H.O. / Friedrich, M.V.K. / Timpl, R. / Sasaki, T. / Hohenester, E. #1: Journal: Embo J. / Year: 2000 Title: Structure of the C-Terminal Laminin G-Like Domain Pair of the Laminin Alpha 2 Chain Harbouring Bindin Sites for Alpha-Dystroglycan and Heparin Authors: Tisi, D. / Talts, J.F. / Timpl, R. / Hohenester, E. #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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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1okq.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1okq.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 1okq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/1okq ftp://data.pdbj.org/pub/pdb/validation_reports/ok/1okq | HTTPS FTP |
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-Related structure data
Related structure data | 1dykS 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: 42655.551 Da / Num. of mol.: 1 Fragment: LAMININ G-LIKE DOMAIN 4-5 PAIR, RESIDUES 2729-3093 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: FVB/N / Tissue: EMBRYO / Cell: EMRYONIC KIDNEY CELL / Cell line: EBNA-293 / Plasmid: PCEP-PU / Cell line (production host): EBNA-293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q60675 | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | D8080A/D2876A DOUBLE MUTANT THE SWISSPROT SEQUENCE IS TAKEN FROM BERNIER S.M., UTANI A., SUGIYAMA S. ...D8080A/D2876A DOUBLE MUTANT 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: 2.82 Å3/Da / Density % sol: 56.34 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 14, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 11824 / % possible obs: 97.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 7.3 / % possible all: 97.3 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.101 |
Reflection shell | *PLUS % possible obs: 97.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.23 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DYK Resolution: 2.8→20 Å / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. reflection obs: 10606 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.3 |