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Open data
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Basic information
Entry | Database: PDB / ID: 3zyg | ||||||
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Title | NETRING2 LAM AND EGF1 DOMAINS | ||||||
![]() | NETRIN-G2 | ||||||
![]() | CELL ADHESION / SYNAPSE | ||||||
Function / homology | ![]() regulation of neuron projection arborization / postsynaptic specialization assembly / Post-translational modification: synthesis of GPI-anchored proteins / synaptic membrane adhesion / regulation of neuron migration / regulation of neuron projection development / regulation of presynapse assembly / side of membrane / presynaptic active zone membrane / axonogenesis ...regulation of neuron projection arborization / postsynaptic specialization assembly / Post-translational modification: synthesis of GPI-anchored proteins / synaptic membrane adhesion / regulation of neuron migration / regulation of neuron projection development / regulation of presynapse assembly / side of membrane / presynaptic active zone membrane / axonogenesis / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / axon / glutamatergic synapse / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seiradake, E. / Coles, C.H. / Perestenko, P.V. / Harlos, K. / Mcilhinney, R.A.J. / Aricescu, A.R. / Jones, E.Y. | ||||||
![]() | ![]() Title: Structural Basis for Cell Surface Patterning Through Netring-Ngl Interactions. Authors: Seiradake, E. / Coles, C.H. / Perestenko, P.V. / Harlos, K. / Mcilhinney, R.A.J. / Aricescu, A.R. / Jones, E.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 265.1 KB | Display | ![]() |
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PDB format | ![]() | 213.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3zyiC ![]() 3zyjC ![]() 3zynC ![]() 3zyoC ![]() 1tvgS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40685.191 Da / Num. of mol.: 2 / Fragment: LAM AND EGF1 DOMAINS, RESIDUES 423-767 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Sugar | ChemComp-NAG / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | N-TERMINAL SECRETION SIGNAL IS CLEAVED DURING PROTEIN PRODUCTION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.69 % / Description: NONE |
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Crystal grow | Details: 20% MME550, 0.1M NACL, 0.1M BICINE PH9 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC CCD / Detector: CCD | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→29.2 Å / Num. obs: 42208 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.32 / Net I/σ(I): 6.4 | |||||||||
Reflection shell | Resolution: 2.2→2.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.35 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TVG Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 13.952 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT PRESENT IN THE INPUT.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.277 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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