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- PDB-6phn: Crystal structure of glucagon analog composed of D-amino acids wi... -

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Basic information

Entry
Database: PDB / ID: 6phn
TitleCrystal structure of glucagon analog composed of D-amino acids with mono-stereoinversion at position 23 (L-Val23) in space group I41 at 1.33 A resolution
ComponentsD-glucagon L-Val23
KeywordsHORMONE / glucagon / GPCR ligand / peptide hormone
Function / homologypolypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsMroz, P.A. / Gonzalez-Gutierrez, G. / DiMarchi, R.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentIndiana University Internal grant United States
Citation
Journal: To Be Published
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
DepositionJun 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-glucagon L-Val23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5092
Polymers3,4861
Non-polymers231
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area2680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.956, 39.956, 38.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-101-

NA

21A-229-

HOH

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Components

#1: Polypeptide(D) D-glucagon L-Val23


Mass: 3485.774 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.5 M sodium chloride, 0.1 M imidazole, pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 20, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.33→28.25 Å / Num. obs: 7026 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Rsym value: 0.051 / Net I/σ(I): 20.6
Reflection shellResolution: 1.33→1.38 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 748 / CC1/2: 0.629 / Rpim(I) all: 0.422 / Rrim(I) all: 0.998 / Rsym value: 0.901 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15_3459: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6PHO

6pho


Resolution: 1.33→28.25 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.96
RfactorNum. reflection% reflection
Rfree0.19 438 6.25 %
Rwork0.1612 --
obs0.1634 7008 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.33→28.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms214 0 1 44 259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004258
X-RAY DIFFRACTIONf_angle_d0.693353
X-RAY DIFFRACTIONf_dihedral_angle_d0.1092
X-RAY DIFFRACTIONf_chiral_restr0.02934
X-RAY DIFFRACTIONf_plane_restr0.00348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.52250.18331310.15482179X-RAY DIFFRACTION100
1.5225-1.91810.19051320.17712221X-RAY DIFFRACTION100
1.9181-28.25950.19061750.1572170X-RAY DIFFRACTION99

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