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- PDB-6phq: Crystal structure of glucagon analog fully composed of D-amino ac... -

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Basic information

Entry
Database: PDB / ID: 6phq
TitleCrystal structure of glucagon analog fully composed of D-amino acids with 4-bromo-D-phenylalanine substitutions at position 6 and 22 in space group I41 at 1.1 A resolution
ComponentsD-glucagon D-BrPhe 6,22
KeywordsHORMONE / glucagon / GPCR ligand / peptide hormone
Function / homologypolypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.32 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 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-glucagon D-BrPhe 6,22


Theoretical massNumber of molelcules
Total (without water)3,2901
Polymers3,2901
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-1 kcal/mol
Surface area2900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.770, 41.770, 30.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Polypeptide(D) D-glucagon D-BrPhe 6,22


Mass: 3290.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium chloride, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9184 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 16, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.32→20.88 Å / Num. obs: 6050 / % possible obs: 98 % / Redundancy: 22.6 % / CC1/2: 0.999 / Rpim(I) all: 0.016 / Rrim(I) all: 0.063 / Rsym value: 0.061 / Net I/σ(I): 26.8
Reflection shellResolution: 1.32→1.45 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1512 / CC1/2: 0.737 / Rpim(I) all: 0.522 / Rrim(I) all: 1.459 / Rsym value: 1.407 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15_3459: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.32→20.88 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2473 553 -
Rwork0.1988 --
obs0.2009 6042 98 %
Refinement stepCycle: LAST / Resolution: 1.32→20.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms223 0 0 20 243
LS refinement shellResolution: 1.32→1.45 Å / Num. reflection obs: 2810

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