2WTH

Low resolution 3D structure of C.elegans globin-like protein (GLB-1): P3121 crystal form

• PDB DOI: https://doi.org/10.2210/pdb2WTH/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-09-16 Released: 2010-04-21 
• Deposition Author(s): Geuens, E., Hoogewijs, D., Nardini, M., Vinck, E., Pesce, A., Kiger, L., Fago, A., Tilleman, L., De Henau, S., Marden, M., Weber, R.E., Van Doorslaer, S., Vanfleteren, J., Moens, L., Bolognesi, M., Dewilde, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.319 
• R-Value Work: 0.269 
• R-Value Observed: 0.271 

Literature

Globin-Like Proteins in Caenorhabditis Elegans: In Vivo Localization, Ligand Binding and Structural Properties.

Geuens, E., Hoogewijs, D., Nardini, M., Vinck, E., Pesce, A., Kiger, L., Fago, A., Tilleman, L., De Henau, S., Marden, M., Weber, R.E., Van Doorslaer, S., Vanfleteren, J., Moens, L., Bolognesi, M., Dewilde, S.

(2010) BMC Biochem 11: 17

• PubMed: 20361867 
• DOI: https://doi.org/10.1186/1471-2091-11-17
• Primary Citation of Related Structures:  
  2WTG, 2WTH


• PubMed Abstract: 
  

  The genome of the nematode Caenorhabditis elegans contains more than 30 putative globin genes that all are transcribed. Although their translated amino acid sequences fit the globin fold, a variety of amino-acid substitutions and extensions generate a wide structural diversity among the putative globins. No information is available on the physicochemical properties and the in vivo expression.

---

Organizational Affiliation: 

Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.

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)

Macromolecule Content

• Total Structure Weight: 39.16 kDa 
• Atom Count: 2,775 
• Modelled Residue Count: 316 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLOBIN-LIKE PROTEIN	A, B	159	Caenorhabditis elegans	Mutation(s): 1
UniProt
Find proteins for P30627 (Caenorhabditis elegans) Explore P30627  Go to UniProtKB:  P30627

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], H [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	E [auth A], J [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], K [auth B], L [auth B], N [auth B], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
OXY	D [auth A], I [auth B]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.319 
• R-Value Work: 0.269 
• R-Value Observed: 0.271 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.681	α = 90
b = 77.681	β = 90
c = 145.64	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-21 
Deposition Author(s): Geuens, E., Hoogewijs, D., Nardini, M., Vinck, E., Pesce, A., Kiger, L., Fago, A., Tilleman, L., De Henau, S., Marden, M., Weber, R.E., Van Doorslaer, S., Vanfleteren, J., Moens, L., Bolognesi, M., Dewilde, S.

Revision History  

• Version 1.0: 2010-04-21
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description