+Open data
-Basic information
Entry | Database: PDB / ID: 4v2b | ||||||
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Title | rat Unc5D Ig domain 1 | ||||||
Components | PROTEIN UNC5D | ||||||
Keywords | APOPTOSIS / UNCOORDINATED-5 / IG DOMAIN / NETRIN RECEPTOR / FLRT | ||||||
Function / homology | Function and homology information netrin receptor activity / regulation of neuron migration / cell-cell adhesion via plasma-membrane adhesion molecules / pyramidal neuron differentiation / axon guidance / apoptotic process / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å | ||||||
Authors | Seiradake, E. / del Toro, D. / Nagel, D. / Cop, F. / Haertl, R. / Ruff, T. / Seyit-Bremer, G. / Harlos, K. / Border, E.C. / Acker-Palmer, A. ...Seiradake, E. / del Toro, D. / Nagel, D. / Cop, F. / Haertl, R. / Ruff, T. / Seyit-Bremer, G. / Harlos, K. / Border, E.C. / Acker-Palmer, A. / Jones, E.Y. / Klein, R. | ||||||
Citation | Journal: Neuron / Year: 2014 Title: Flrt Structure: Balancing Repulsion and Cell Adhesion in Cortical and Vascular Development Authors: Seiradake, E. / Del Toro, D. / Nagel, D. / Cop, F. / Haertl, R. / Ruff, T. / Seyit-Bremer, G. / Harlos, K. / Border, E.C. / Acker-Palmer, A. / Jones, E.Y. / Klein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v2b.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v2b.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 4v2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/4v2b ftp://data.pdbj.org/pub/pdb/validation_reports/v2/4v2b | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18128.379 Da / Num. of mol.: 2 / Fragment: IG DOMAIN 1, RESIDUES 1-161 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Production host: HOMO SAPIENS (human) / References: UniProt: F1LW30 #2: Water | ChemComp-HOH / | Sequence details | N-TERMINUS IS PROTEOLYTI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.26 % / Description: NONE |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2→61 Å / Num. obs: 410812 / % possible obs: 99.8 % / Redundancy: 18 % / Biso Wilson estimate: 58.74 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.63 | |||||||||||||||
Reflection shell | Resolution: 2→2.2 Å / Redundancy: 19.3 % / Mean I/σ(I) obs: 0.67 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: NONE Resolution: 2→60.72 Å / Cor.coef. Fo:Fc: 0.8847 / Cor.coef. Fo:Fc free: 0.8783 / SU R Cruickshank DPI: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.224 / SU Rfree Blow DPI: 0.189 / SU Rfree Cruickshank DPI: 0.189
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Displacement parameters | Biso mean: 88.44 Å2
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Refine analyze | Luzzati coordinate error obs: 0.815 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→60.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.1 Å / Total num. of bins used: 11
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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