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- PDB-4xhq: Re-refinement the crystal structure of Dscam1 isoform 1.34, N-ter... -
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Open data
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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 | |||||||||
![]() | Dscam | |||||||||
![]() | CELL ADHESION / Ig fold | |||||||||
Function / homology | ![]() DSCAM interactions / detection of molecule of bacterial origin / mushroom body development / detection of mechanical stimulus involved in sensory perception of touch / central nervous system morphogenesis / ventral cord development / axon extension involved in axon guidance / axon guidance receptor activity / dendrite self-avoidance / cell-cell adhesion mediator activity ...DSCAM interactions / detection of molecule of bacterial origin / mushroom body development / detection of mechanical stimulus involved in sensory perception of touch / central nervous system morphogenesis / ventral cord development / axon extension involved in axon guidance / axon guidance receptor activity / dendrite self-avoidance / cell-cell adhesion mediator 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 / central nervous system development / 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 | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Chen, Q. / Yu, Y. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.7 KB | Display | ![]() |
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PDB format | ![]() | 78.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 32.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wvrC ![]() 4x5lC ![]() 4x83C ![]() 4x8xC ![]() 4x9bC ![]() 4x9fC ![]() 4x9gC ![]() 4x9hC ![]() 4x9iC ![]() 4xb7C ![]() 4xb8C C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() |
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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 ![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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 |
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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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