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- PDB-5nks: Human Dihydropyrimidinase-related Protein 4 (DPYSL4, CRMP3, ULIP-4) -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nks | ||||||
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Title | Human Dihydropyrimidinase-related Protein 4 (DPYSL4, CRMP3, ULIP-4) | ||||||
![]() | Dihydropyrimidinase-related protein 4 | ||||||
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Function / homology | ![]() : / neuron projection guidance / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mathea, S. / Elkins, J.M. / Strain-Damerell, C. / Salah, E. / Borkowska, O. / Chalk, R. / Burgess-Brown, N. / Pinkas, D.M. / von Delft, F. / Krojer, T. ...Mathea, S. / Elkins, J.M. / Strain-Damerell, C. / Salah, E. / Borkowska, O. / Chalk, R. / Burgess-Brown, N. / Pinkas, D.M. / von Delft, F. / Krojer, T. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. | ||||||
![]() | ![]() Title: Human Dihydropyrimidinase-related Protein 4 (DPYSL4, CRMP3, ULIP-4) Authors: Mathea, S. / Knapp, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.9 KB | Display | ![]() |
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PDB format | ![]() | 86.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4bknS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 62043.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.82 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Bis-tris-propane 0.2 M Sodium fluoride 10% Ethylene glycol 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→27.85 Å / Num. obs: 44328 / % possible obs: 98.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2 / Num. unique obs: 2548 / % possible all: 96.6 |
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Processing
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Refinement | Starting model: 4BKN Resolution: 1.8→77.16 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.332 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.115 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.729 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→77.16 Å
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Refine LS restraints |
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