+Open data
-Basic information
Entry | Database: PDB / ID: 2v5s | |||||||||
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Title | Structural basis for Dscam isoform specificity | |||||||||
Components | DSCAM | |||||||||
Keywords | CELL ADHESION / DOWN SYNDROME / IMMUNOGLOBULIN DOMAIN / MEMBRANE / DEVELOPMENTAL PROTEIN | |||||||||
Function / homology | Function and homology information DSCAM interactions / detection of molecule of bacterial origin / mushroom body development / central nervous system morphogenesis / detection of mechanical stimulus involved in sensory perception of touch / ventral cord development / dendrite self-avoidance / axon extension involved in axon guidance / axon guidance receptor activity / cell-cell adhesion mediator activity ...DSCAM interactions / detection of molecule of bacterial origin / mushroom body development / central nervous system morphogenesis / detection of mechanical stimulus involved in sensory perception of touch / ventral cord development / dendrite self-avoidance / axon extension involved in axon guidance / axon guidance receptor activity / cell-cell adhesion mediator activity / peripheral nervous system development / axonal fasciculation / regulation of axonogenesis / regulation of dendrite morphogenesis / 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 | DROSOPHILA MELANOGASTER (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Meijers, R. / Puettmann-Holgado, R. / Skiniotis, G. / Liu, J.-H. / Walz, T. / Schmucker, D. / Wang, J.-H. | |||||||||
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 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 | 2v5s.cif.gz | 177.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v5s.ent.gz | 141.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v5s_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 2v5s_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 2v5s_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 2v5s_validation.cif.gz | 52.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/2v5s ftp://data.pdbj.org/pub/pdb/validation_reports/v5/2v5s | HTTPS FTP |
-Related structure data
Related structure data | 2v5mSC 2v5rC S: Starting model for refinement 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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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: |
-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.) DROSOPHILA MELANOGASTER (fruit fly) / Organ: BRAIN / Variant: SPLICING VARIANT 4.1/6.34 / Plasmid: BACNBLUE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NBA1 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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