4GN0

De novo phasing of a Hamp-complex using an improved Arcimboldo method

• PDB DOI: https://doi.org/10.2210/pdb4GN0/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Archaeoglobus fulgidus DSM 4304
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-08-16 Released: 2013-09-11 
• Deposition Author(s): Hulko, M., Ursinus, A., Bar, K., Martin, J., Zeth, K., Lupas, A.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.224 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

Exploiting tertiary structure through local folds for crystallographic phasing.

Sammito, M., Millan, C., Rodriguez, D.D., de Ilarduya, I.M., Meindl, K., De Marino, I., Petrillo, G., Buey, R.M., de Pereda, J.M., Zeth, K., Sheldrick, G.M., Uson, I.

(2013) Nat Methods 10: 1099-1101

• PubMed: 24037245 
• DOI: https://doi.org/10.1038/nmeth.2644
• Primary Citation of Related Structures:  
  4GDO, 4GN0


• PubMed Abstract: 
  

  We describe an algorithm for phasing protein crystal X-ray diffraction data that identifies, retrieves, refines and exploits general tertiary structural information from small fragments available in the Protein Data Bank. The algorithm successfully phased, through unspecific molecular replacement combined with density modification, all-helical, mixed alpha-beta, and all-beta protein structures. The method is available as a software implementation: Borges.

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Organizational Affiliation: 

Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Spain.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.58 kDa 
• Atom Count: 3,503 
• Modelled Residue Count: 412 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hamp domain of AF1503	A, B, C, D	105	Archaeoglobus fulgidus DSM 4304	Mutation(s): 14  Gene Names: AF_1503
UniProt
Find proteins for O28769 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28769  Go to UniProtKB:  O28769

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.224 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.115	α = 90
b = 48.077	β = 98.02
c = 95.262	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Hulko, M., Ursinus, A., Bar, K., Martin, J., Zeth, K., Lupas, A.N.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2013-09-25
  Changes: Database references
• Version 1.2: 2013-11-20
  Changes: Database references
• Version 1.3: 2014-01-22
  Changes: Structure summary
• Version 1.4: 2014-03-19
  Changes: Structure summary
• Version 1.5: 2024-02-28
  Changes: Data collection, Database references, Derived calculations