1HDF

Evolution of the eye lens beta-gamma-crystallin domain fold

• PDB DOI: https://doi.org/10.2210/pdb1HDF/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Physarum polycephalum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-11-13 Released: 2000-12-28 
• Deposition Author(s): Clout, N.J., Kretschmar, M., Jaenicke, R., Slingsby, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Work: 0.239 
• R-Value Observed: 0.239 

Literature

Crystal Structure of the Calcium-Loaded Spherulin 3A Dimer Sheds Light on the Evolution of the Eye Lens Betagamma-Crystallin Domain Fold

Clout, N.J., Kretschmar, M., Jaenicke, R., Slingsby, C.

(2001) Structure 9: 115

• PubMed: 11250196 
• DOI: https://doi.org/10.1016/s0969-2126(01)00573-1
• Primary Citation of Related Structures:  
  1HDF


• PubMed Abstract: 
  

  The betagamma-crystallins belong to a superfamily of two-domain proteins found in vertebrate eye lenses, with distant relatives occurring in microorganisms. It has been considered that an eukaryotic stress protein, spherulin 3a, from the slime mold Physarum polycephalum shares a common one-domain ancestor with crystallins, similar to the one-domain 3-D structure determined by NMR.

---

Organizational Affiliation: 

Department of Crystallography, Birkbeck College, Malet Street, WC1E 7HX, London, United Kingdom.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 22.62 kDa 
• Atom Count: 1,675 
• Modelled Residue Count: 200 
• Deposited Residue Count: 204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPHERULIN 3A	A, B	102	Physarum polycephalum	Mutation(s): 1
UniProt
Find proteins for P09353 (Physarum polycephalum) Explore P09353  Go to UniProtKB:  P09353

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Work: 0.239 
• R-Value Observed: 0.239 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.35	α = 90
b = 41.35	β = 90
c = 213.64	γ = 90

Software Package:

Software Name	Purpose
CNS	phasing
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-28 
Deposition Author(s): Clout, N.J., Kretschmar, M., Jaenicke, R., Slingsby, C.

Revision History  

• Version 1.0: 2000-12-28
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance