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Open data
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Basic information
Entry | Database: PDB / ID: 2v5s | |||||||||
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Title | Structural basis for Dscam isoform specificity | |||||||||
![]() | DSCAM | |||||||||
![]() | CELL ADHESION / DOWN SYNDROME / IMMUNOGLOBULIN DOMAIN / MEMBRANE / DEVELOPMENTAL PROTEIN | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Meijers, R. / Puettmann-Holgado, R. / Skiniotis, G. / Liu, J.-H. / Walz, T. / Schmucker, D. / Wang, J.-H. | |||||||||
![]() | ![]() 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 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.9 KB | Display | ![]() |
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PDB format | ![]() | 141.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 37.6 KB | Display | |
Data in CIF | ![]() | 52.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2v5mSC ![]() 2v5rC S: Starting model for refinement 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 5 / Auth seq-ID: 1 - 388 / Label seq-ID: 7 - 394
NCS oper: (Code: given Matrix: (0.99985, -0.00253, 0.01723), Vector: |
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Components
#1: Protein | Mass: 43562.273 Da / Num. of mol.: 2 Fragment: N-TERMINAL FOUR DOMAINS (D1, D2, D3 AND D4), RESIDUES 36-423 Source method: isolated from a genetically manipulated source Details: ISOFORM 4.1/6.34 / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | Sequence details | THE CONFLICTS GIVEN IN THE SEQADV RECORDS BELOW ARE AS A RESULT OF A SPLICE VARIANT FORM OF THE ...THE CONFLICTS GIVEN IN THE SEQADV RECORDS BELOW ARE AS A RESULT OF A SPLICE VARIANT FORM OF THE PROTEIN WHERE EXON 4 COVERING RESIDUES 102 TO 156 CONSISTS OF ISOFORM 1 AND EXON 6 COVERING RESIDUES 205 TO 245 CONSISTS OF ISOFORM 34. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE |
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Crystal grow | Details: 1.5 M AMMONIUM SULPHATE 0.1 M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 22250 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.3→2.35 Å / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2 / % possible all: 93.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2V5M Resolution: 2.3→19.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 20.095 / SU ML: 0.24 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.17 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.99 Å
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Refine LS restraints |
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