7QGF | pdb_00007qgf

Cubic Insulin SAD phasing at 14.2 keV

• PDB DOI: https://doi.org/10.2210/pdb7QGF/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2021-12-08 Released: 2022-06-01 
• Deposition Author(s): Nanao, M.H., Basu, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.165 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.148 (DCC) 

Literature

ID23-2: an automated and high-performance microfocus beamline for macromolecular crystallography at the ESRF.

Nanao, M., Basu, S., Zander, U., Giraud, T., Surr, J., Guijarro, M., Lentini, M., Felisaz, F., Sinoir, J., Morawe, C., Vivo, A., Beteva, A., Oscarsson, M., Caserotto, H., Dobias, F., Flot, D., Nurizzo, D., Gigmes, J., Foos, N., Siebrecht, R., Roth, T., Theveneau, P., Svensson, O., Papp, G., Lavault, B., Cipriani, F., Barrett, R., Clavel, C., Leonard, G.

(2022) J Synchrotron Radiat 29: 581-590

• PubMed: 35254323 
• DOI: https://doi.org/10.1107/S1600577522000984
• Primary Citation Related Structures: 
  7QGF


• PubMed Abstract: 
  

  ID23-2 is a fixed-energy (14.2 keV) microfocus beamline at the European Synchrotron Radiation Facility (ESRF) dedicated to macromolecular crystallography. The optics and sample environment have recently been redesigned and rebuilt to take full advantage of the upgrade of the ESRF to the fourth generation Extremely Brilliant Source (ESRF-EBS). The upgraded beamline now makes use of two sets of compound refractive lenses and multilayer mirrors to obtain a highly intense (>10 ¹³  photons s ^-1 ) focused microbeam (minimum size 1.5 µm × 3 µm full width at half-maximum). The sample environment now includes a FLEX-HCD sample changer/storage system, as well as a state-of-the-art MD3Up high-precision multi-axis diffractometer. Automatic data reduction and analysis are also provided for more advanced protocols such as synchrotron serial crystallographic experiments.

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Organizational Affiliation: 
• European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France.
European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France.
ARINAX, 365 Rue de Corporat, 38430 Moirans, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.72 kDa 
• Atom Count: 457 
• Modeled Residue Count: 50 
• Deposited Residue Count: 50 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin A chain	A [auth AAA]	21	Homo sapiens	Mutation(s): 0  Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308
PHAROS:  P01308 GTEx:  ENSG00000254647

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin B chain	B [auth BBB]	29	Homo sapiens	Mutation(s): 0  Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308
PHAROS:  P01308 GTEx:  ENSG00000254647

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.165 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.148 (DCC) 

Diffraction Data: https://doi.org/10.5281/zenodo.5761266

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.562	α = 90
b = 78.562	β = 90
c = 78.562	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELXCD	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Nanao, M.H., Basu, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Derived calculations, Structure summary