+Open data
-Basic information
Entry | Database: PDB / ID: 2vr9 | ||||||
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Title | Drosophila Robo IG1-2 (tetragonal form) | ||||||
Components | ROUNDABOUT 1 | ||||||
Keywords | CELL ADHESION / IMMUNOGLOBULIN-LIKE DOMAIN / AXON GUIDANCE / IMMUNOGLOBULIN DOMAIN | ||||||
Function / homology | Function and homology information Slit-Robo signaling complex / dendrite guidance / regulation of epithelial cell migration, open tracheal system / salivary gland boundary specification / photoreceptor cell axon guidance / neuron recognition / gonad development / axon guidance receptor activity / cell-cell adhesion mediator activity / regulation of dendrite development ...Slit-Robo signaling complex / dendrite guidance / regulation of epithelial cell migration, open tracheal system / salivary gland boundary specification / photoreceptor cell axon guidance / neuron recognition / gonad development / axon guidance receptor activity / cell-cell adhesion mediator activity / regulation of dendrite development / positive regulation of cell-cell adhesion / Roundabout signaling pathway / entrainment of circadian clock / embryonic heart tube development / motor neuron axon guidance / axon midline choice point recognition / dendrite morphogenesis / muscle cell cellular homeostasis / outflow tract morphogenesis / axonal growth cone / axon guidance / brain development / heparin binding / vesicle / neuron projection / axon / neuronal cell body / dendrite / protein-containing complex / plasma membrane Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Fukuhara, N. / Howitt, J.A. / Hussain, S. / Hohenester, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structural and Functional Analysis of Slit and Heparin Binding to Immunoglobulin-Like Domains 1 and 2 of Drosophila Robo Authors: Fukuhara, N. / Howitt, J.A. / Hussain, S. / Hohenester, E. | ||||||
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 | 2vr9.cif.gz | 122.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vr9.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vr9_validation.pdf.gz | 440.1 KB | Display | wwPDB validaton report |
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Full document | 2vr9_full_validation.pdf.gz | 453.3 KB | Display | |
Data in XML | 2vr9_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 2vr9_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/2vr9 ftp://data.pdbj.org/pub/pdb/validation_reports/vr/2vr9 | HTTPS FTP |
-Related structure data
Related structure data | 2vraC 2iepS C: citing same article (ref.) 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 24135.492 Da / Num. of mol.: 3 / Fragment: IG1-2, RESIDUES 51-254 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: O44924 Sequence details | N-TERMINAL APLA AND C-TERMINAL AAAHHHHHH, VECTOR DERIVED | |
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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: 3.35 Å3/Da / Density % sol: 63 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 5, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. obs: 15618 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 78 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IEP Resolution: 3.2→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.6862 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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Xplor file |
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