+Open data
-Basic information
Entry | Database: PDB / ID: 2wfv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of DILP5 variant C4 | ||||||
Components |
| ||||||
Keywords | SIGNALING PROTEIN / CLEAVAGE ON PAIR OF BASIC RESIDUES | ||||||
Function / homology | Function and homology information negative regulation of entry into reproductive diapause / Insulin signaling pathway / female mating behavior / carbohydrate homeostasis / sleep / locomotory behavior / insulin receptor binding / hormone activity / insulin receptor signaling pathway / receptor ligand activity ...negative regulation of entry into reproductive diapause / Insulin signaling pathway / female mating behavior / carbohydrate homeostasis / sleep / locomotory behavior / insulin receptor binding / hormone activity / insulin receptor signaling pathway / receptor ligand activity / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.85 Å | ||||||
Authors | Kulahin, N. / Schluckebier, G. / Sajid, W. / De Meyts, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural and Biological Properties of the Drosophila Insulin-Like Peptide 5 Show Evolutionary Conservation. Authors: Sajid, W. / Kulahin, N. / Schluckebier, G. / Ribel, U. / Henderson, H.R. / Tatar, M. / Hansen, B.F. / Svendsen, A.M. / Kiselyov, V.V. / Norgaard, P. / Wahlund, P. / Brandt, J. / Kohanski, R. ...Authors: Sajid, W. / Kulahin, N. / Schluckebier, G. / Ribel, U. / Henderson, H.R. / Tatar, M. / Hansen, B.F. / Svendsen, A.M. / Kiselyov, V.V. / Norgaard, P. / Wahlund, P. / Brandt, J. / Kohanski, R.A. / Andersen, A.S. / De Meyts, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2wfv.cif.gz | 17.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2wfv.ent.gz | 13.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wfv_validation.pdf.gz | 422.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2wfv_full_validation.pdf.gz | 423.9 KB | Display | |
Data in XML | 2wfv_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 2wfv_validation.cif.gz | 5.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/2wfv ftp://data.pdbj.org/pub/pdb/validation_reports/wf/2wfv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 2795.097 Da / Num. of mol.: 1 / Fragment: RESIDUES 84-108 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q7KUD5 | ||
---|---|---|---|
#2: Protein/peptide | Mass: 2452.898 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-46 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q7KUD5 | ||
#3: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | LYS12A HAS BEEN MUTATED TO ASN12A AS A PART OF CLONING STRATEGY | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.59 Å3/Da / Density % sol: 23 % / Description: NONE |
---|---|
Crystal grow | Details: 20% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→24.18 Å / Num. obs: 3164 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 56 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.54 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 1.85→24.18 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.179 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 29.54 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→24.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|