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Yorodumi- PDB-3ins: STRUCTURE OF INSULIN. RESULTS OF JOINT NEUTRON AND X-RAY REFINEMENT -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ins | ||||||
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Title | STRUCTURE OF INSULIN. RESULTS OF JOINT NEUTRON AND X-RAY REFINEMENT | ||||||
Components |
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Keywords | HORMONE | ||||||
Function / homology | Function and homology information Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine ...Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine / positive regulation of lipoprotein lipase activity / lactate biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / lipid biosynthetic process / positive regulation of DNA replication / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / positive regulation of protein secretion / hormone activity / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / positive regulation of cell migration / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / NEUTRON DIFFRACTION / Resolution: 1.5 Å | ||||||
Authors | Wlodawer, A. / Savage, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.B / Year: 1989 Title: Structure of insulin: results of joint neutron and X-ray refinement. Authors: Wlodawer, A. / Savage, H. / Dodson, G. #1: Journal: Acta Crystallogr.,Sect.A / Year: 1978 Title: Experience with Fast Fourier Least Squares in the Refinement of the Crystal Structure of Rhombohedral 2-Zinc Insulin at 1.5 Angstroms Resolution Authors: Isaacs, N.W. / Agarwal, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ins.cif.gz | 56.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ins.ent.gz | 43.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ins.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ins_validation.pdf.gz | 411.3 KB | Display | wwPDB validaton report |
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Full document | 3ins_full_validation.pdf.gz | 420.8 KB | Display | |
Data in XML | 3ins_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 3ins_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/3ins ftp://data.pdbj.org/pub/pdb/validation_reports/in/3ins | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Atom site foot note | 1: THE FOLLOWING RESIDUES ARE DISORDERED - VAL B 12, GLU B 21, ARG B 22, THR B 27, ARG D 22, LYS D 29. 2: DISORDER IN RESIDUE VAL B 12 PRECLUDES USE OF STANDARD NOMENCLATURE FOR HYDROGEN ATOMS IN THIS RESIDUE. THE HYDROGEN ATOMS, THEREFORE, ARE ARBITRARILY NAMED. ALSO SEE FTNOTE 1. | |||||||||||||||
Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.87862, -0.47696, 0.02305), Details | THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT OF INSULIN CONSISTS OF TWO INSULIN MOLECULES EACH CONSISTING OF TWO CHAINS. THIS ENTRY PRESENTS COORDINATES FOR MOLECULES I (CHAIN INDICATORS A AND B) AND II (CHAIN INDICATORS C AND D). THE QUASI-TWO-FOLD AXIS THAT TRANSFORMS MOLECULE I INTO MOLECULE II IS GIVEN IN THE MTRIX RECORDS BELOW. APPLYING THE THREE-FOLD CRYSTALLOGRAPHIC AXIS YIELDS A HEXAMER AROUND THE AXIS. THERE ARE TWO ZINC IONS SITUATED ON THIS THREE-FOLD AXIS. COORDINATES FOR THE ZINC IONS AND WATER MOLECULES ARE INCLUDED BELOW WITH A BLANK CHAIN INDICATOR. | |
-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P01315 #2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P01315 #3: Chemical | #4: Chemical | ChemComp-DOD / | |
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-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.05 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation wavelength | Relative weight: 1 |
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Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Observed criterion σ(F): 0 / Num. measured all: 13476 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement |
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Refinement step | Cycle: LAST / Highest resolution: 1.5 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |