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Yorodumi- PDB-8edi: Structure of C. elegans UNC-5 IG 1+2 Domains bound to Heparin dp4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8edi | |||||||||
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Title | Structure of C. elegans UNC-5 IG 1+2 Domains bound to Heparin dp4 | |||||||||
Components | Netrin receptor unc-5 | |||||||||
Keywords | PROTEIN BINDING / Cell surface receptor / Axon Guidance / Signaling / Glycoprotein | |||||||||
Function / homology | Function and homology information distal tip cell migration / Netrin-1 signaling / positive regulation of anterior/posterior axon guidance / regulation of dorsal/ventral axon guidance / mesodermal cell migration / gonad morphogenesis / positive regulation of locomotion / nematode male tail tip morphogenesis / netrin receptor activity / dorsal/ventral axon guidance ...distal tip cell migration / Netrin-1 signaling / positive regulation of anterior/posterior axon guidance / regulation of dorsal/ventral axon guidance / mesodermal cell migration / gonad morphogenesis / positive regulation of locomotion / nematode male tail tip morphogenesis / netrin receptor activity / dorsal/ventral axon guidance / chemorepulsion of axon / netrin-activated signaling pathway / establishment or maintenance of actin cytoskeleton polarity / ventral cord development / commissural neuron axon guidance / motor neuron axon guidance / negative regulation of microtubule polymerization / positive regulation of axon extension / axonal growth cone / protein tyrosine kinase binding / membrane raft / plasma membrane Similarity search - Function | |||||||||
Biological species | Caenorhabditis elegans (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | |||||||||
Authors | Priest, J.M. / Ozkan, E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Structure of C. elegans UNC-5 IG 1+2 Domains Authors: Priest, J.M. / Ozkan, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8edi.cif.gz | 214.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8edi.ent.gz | 144.6 KB | Display | PDB format |
PDBx/mmJSON format | 8edi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/8edi ftp://data.pdbj.org/pub/pdb/validation_reports/ed/8edi | HTTPS FTP |
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-Related structure data
Related structure data | 8edcSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.535665366599, -0.842344850865, 0.0593107683968), (-0.841123208806, 0.526039550849, -0.125674733142), (0.0746616543779, -0.117207265831, -0.990296972732)Vector: 4. ...NCS oper: (Code: given Matrix: (-0.535665366599, -0.842344850865, 0.0593107683968), Vector: |
-Components
#1: Protein | Mass: 23186.814 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-5, B0273.4 / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q26261 #2: Polysaccharide | #3: Polysaccharide | 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)- ...4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose | Type: oligosaccharide / Mass: 1154.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.36 Å3/Da / Density % sol: 63.39 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 4% (v/v) Pentaerythritol ethoxylate (3/4 EO/OH), 0.1 M sodium acetate pH 4.6, 16% (w/v) PEG 8000, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033167 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→49.1 Å / Num. obs: 21299 / % possible obs: 58 % / Redundancy: 18.4 % / Biso Wilson estimate: 53.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.014 / Rrim(I) all: 0.061 / Rsym value: 0.059 / Net I/σ(I): 27 |
Reflection shell | Resolution: 2.11→2.3 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.66 / Mean I/σ(I) obs: 2 / Num. unique obs: 1065 / CC1/2: 0.724 / Rpim(I) all: 0.43 / Rrim(I) all: 1.72 / Rsym value: 1.66 / % possible all: 24.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8EDC Resolution: 2.11→49.1 Å / SU ML: 0.3186 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.3254 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→49.1 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.957894604009 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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