[English] 日本語
Yorodumi- PDB-2bf9: Anisotropic refinement of avian (turkey) pancreatic polypeptide a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bf9 | ||||||
---|---|---|---|---|---|---|---|
Title | Anisotropic refinement of avian (turkey) pancreatic polypeptide at 0. 99 Angstroms resolution. | ||||||
Components | PANCREATIC HORMONE | ||||||
Keywords | HORMONE / PANCREATIC HORMONE / TURKEY / PANCREAS / POLYPEPTIDE / ATOMIC RESOLUTION / ANISOTROPIC REFINEMENT | ||||||
Function / homology | Function and homology information neuropeptide Y receptor binding / neuropeptide hormone activity / feeding behavior / neuropeptide signaling pathway / extracellular space Similarity search - Function | ||||||
Biological species | MELEAGRIS GALLOPAVO (turkey) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 0.99 Å | ||||||
Authors | Tickle, I. / Glover, I. / Pitts, J. / Wood, S. / Blundell, T.L. | ||||||
Citation | Journal: Biopolymers / Year: 1983 Title: Conformational Flexibility in a Small Globular Hormone. X-Ray Analysis of Avian Pancreatic Polypeptide at 0.98 Angstroms Resolution Authors: Glover, I. / Haneef, I. / Pitts, J. / Wood, S. / Moss, D. / Tickle, I. / Blundell, T.L. #1: Journal: Kristallografiya / Year: 1982 Title: Crystal Structure Analysis of Avian Pancreatic Polypeptide at 1.37 Angstroms Resolution Authors: Pitts, J.E. / Tickle, I.J. / Wood, S.P. / Blundell, T.L. #2: Journal: Sov.Phys.Crystallogr.(Engl. Transl.) / Year: 1982 Title: Crystal Structure Analysis of Avian Pancreatic Polypeptide at 1.37 Angstroms Resolution Authors: Pitts, J.E. / Tickle, I.J. / Wood, S.P. / Blundell, T.L. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981 Title: X-Ray Analysis (1.4-Angstroms Resolution) of Avian Pancreatic Polypeptide. Small Globular Protein Hormone Authors: Blundell, T.L. / Pitts, J.E. / Tickle, I.J. / Wood, S.P. / Wu, C.-W. #4: Journal: Eur.J.Biochem. / Year: 1977 Title: Purification, Crystallisation and Preliminary X-Ray Studies on Avian Pancreatic Polypeptide Authors: Wood, S.P. / Pitts, J.E. / Blundell, T.L. / Tickle, I.J. / Jenkins, J.A. #5: Journal: J.Biol.Chem. / Year: 1975 Title: Isolation and Characterization of a New Pancreatic Polypeptide Hormone Authors: Kimmel, J.R. / Hayden, L.J. / Pollock, H.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2bf9.cif.gz | 34.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2bf9.ent.gz | 26.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bf9_validation.pdf.gz | 385.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2bf9_full_validation.pdf.gz | 385.4 KB | Display | |
Data in XML | 2bf9_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 2bf9_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/2bf9 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/2bf9 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein/peptide | Mass: 4241.634 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COLLECTED FROM COMMERCIAL UK TURKEY FARM. / Source: (natural) MELEAGRIS GALLOPAVO (turkey) / Cell: ISLETS OF LANGERHANS / Organ: PANCREAS / References: UniProt: P68249 |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
---|
-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.14 % |
---|---|
Crystal grow | pH: 7 Details: 5MG/ML POLYPEPTIDE IN 0.1M TRIS-HCL BUFFER, 0.001M ZN(OAC)2, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SEALED TUBE / Type: HILGER-WATTS 1.2KW / Wavelength: 1.54178 |
Detector | Type: HILGER-WATTS / Detector: Y290 SCINTILLATION COUNTER / Date: Jan 1, 1983 / Details: HELIUM PATH |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 0.99→27.45 Å / Num. obs: 17058 / % possible obs: 94.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS / Resolution: 0.99→27.45 Å / Num. parameters: 3457 / Num. restraintsaints: 1694 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: THIS IS A REFINEMENT OF PDB ENTRY 1PPT USING NEW X-RAY DATA AT ATOMIC RESOLUTION.
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 281 / Occupancy sum non hydrogen: 382.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.99→27.45 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|