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- PDB-6phm: Crystal structure of glucagon analog fully composed of D-amino ac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6phm | ||||||
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Title | Crystal structure of glucagon analog fully composed of D-amino acids in space group I41 at 1.1 A resolution | ||||||
![]() | D-glucagon | ||||||
![]() | HORMONE / glucagon / GPCR ligand / peptide hormone | ||||||
Function / homology | polypeptide(D) / polypeptide(D) (> 10)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mroz, P.A. / Gonzalez-Gutierrez, G. / DiMarchi, R.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: High resolution X-ray structure of glucagon and selected stereo-inversed analogs in novel crystallographic packing arrangement. Authors: Mroz, P.A. / Gonzalez-Gutierrez, G. / DiMarchi, R.D. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / ![]() Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.5 KB | Display | ![]() |
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PDB format | ![]() | 26.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6phiC ![]() 6phjC ![]() 6phkC ![]() 6phlC ![]() 6phnC ![]() 6phoSC ![]() 6phpC ![]() 6phqC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Polypeptide(D) | Mass: 3485.774 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 33.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulfate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Sep 20, 2017 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→29.96 Å / Num. obs: 10382 / % possible obs: 99.3 % / Redundancy: 7.9 % / CC1/2: 0.999 / Rpim(I) all: 0.011 / Rrim(I) all: 0.036 / Rsym value: 0.034 / Net I/σ(I): 39.3 |
Reflection shell | Resolution: 1.1→1.29 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3234 / CC1/2: 0.975 / Rpim(I) all: 0.134 / Rrim(I) all: 0.24 / Rsym value: 0.196 / % possible all: 90.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 6PHO Resolution: 1.1→29.96 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→29.96 Å
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Refine LS restraints |
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LS refinement shell |
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