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Yorodumi- PDB-4xhq: Re-refinement the crystal structure of Dscam1 isoform 1.34, N-ter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xhq | |||||||||
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Title | Re-refinement the crystal structure of Dscam1 isoform 1.34, N-terminal four Ig domains | |||||||||
Components | Dscam | |||||||||
Keywords | CELL ADHESION / Ig fold | |||||||||
Function / homology | Function and homology information DSCAM interactions / mushroom body development / detection of mechanical stimulus involved in sensory perception of touch / detection of molecule of bacterial origin / central nervous system morphogenesis / ventral cord development / dendrite self-avoidance / cell-cell adhesion mediator activity / axon extension involved in axon guidance / axon guidance receptor activity ...DSCAM interactions / mushroom body development / detection of mechanical stimulus involved in sensory perception of touch / detection of molecule of bacterial origin / central nervous system morphogenesis / ventral cord development / dendrite self-avoidance / cell-cell adhesion mediator activity / axon extension involved in axon guidance / axon guidance receptor activity / peripheral nervous system development / axonal fasciculation / regulation of dendrite morphogenesis / regulation of axonogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / neuron development / phagocytosis / antigen binding / axon guidance / perikaryon / neuron projection / axon / neuronal cell body / dendrite / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.948 Å | |||||||||
Authors | Chen, Q. / Yu, Y. | |||||||||
Citation | Journal: NATURE / Year: 2007 Title: Structural Basis of Dscam Isoform Specificity Authors: Meijers, R. / Puettmann-Holgado, R. / Skiniotis, G. / Liu, J.-H. / Walz, T. / Wang, J.-H. / Schmucker, D. | |||||||||
History |
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Remark 0 | THIS ENTRY 4XHQ REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R2V5MSF ORIGINAL DATA ...THIS ENTRY 4XHQ REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R2V5MSF ORIGINAL DATA DETERMINED BY AUTHOR: R.MEIJERS,R.PUETTMANN-HOLGADO,G.SKINIOTIS,J.-H.LIU,T.WALZ, D.SCHMUCKER,J.-H.WANG |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xhq.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xhq.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 4xhq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/4xhq ftp://data.pdbj.org/pub/pdb/validation_reports/xh/4xhq | HTTPS FTP |
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-Related structure data
Related structure data | 4wvrC 4x5lC 4x83C 4x8xC 4x9bC 4x9fC 4x9gC 4x9hC 4x9iC 4xb7C 4xb8C C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42880.582 Da / Num. of mol.: 1 / Fragment: UNP residues 36-423 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dscam1, Dscam, CG17800 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NBA1 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 396 molecules
#4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-NA / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 73.84 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2V5M. |
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Crystal grow | Details: 1.5 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7.5 |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Resolution: 1.948→19.834 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.948→19.834 Å
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Refine LS restraints |
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LS refinement shell |
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