[English] 日本語
Yorodumi- PDB-2w50: N-terminal domain of human conserved dopamine neurotrophic factor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w50 | ||||||
---|---|---|---|---|---|---|---|
Title | N-terminal domain of human conserved dopamine neurotrophic factor (CDNF) | ||||||
Components | ARMET-LIKE PROTEIN 1 | ||||||
Keywords | HORMONE / MANF / CDNF / SAPOSIN / SECRETED / ER STRESS / ALTERNATIVE SPLICING / GROWTH FACTOR / NEUROTROPHIC FACTOR | ||||||
Function / homology | Function and homology information dopaminergic neuron differentiation / growth factor activity / neuron projection development / endoplasmic reticulum / extracellular space Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Parkash, V. / Lindholm, P. / Peranen, J. / Kalkkinen, N. / Oksanen, E. / Saarma, M. / Leppanen, V.M. / Goldman, A. | ||||||
Citation | Journal: Protein Eng.Des.Sel. / Year: 2009 Title: The Structure of the Conserved Neurotrophic Factors Manf and Cdnf Explains Why They are Bifunctional. Authors: Parkash, V. / Lindholm, P. / Peranen, J. / Kalkkinen, N. / Oksanen, E. / Saarma, M. / Leppanen, V.M. / Goldman, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2w50.cif.gz | 49.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2w50.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 2w50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/2w50 ftp://data.pdbj.org/pub/pdb/validation_reports/w5/2w50 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 11750.771 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 32-133 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q49AH0 #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 53 % / Description: NONE |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 4.6 Details: CRYSTALS OF CDNF AT 10-20 MG/ML WERE GROWN IN SITTING DROPS OVER A RESERVOIR SOLUTION OF 100 MM NA-ACETATE, PH 4.6, 0.2 M NH4-ACETATE AND 25-30 % MME-PEG 2000. |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 110661 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.6→1.7 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.991 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 22.27 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|