Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15600.53 
• Atom Count: 1094 
• Residue Count: 147 
• Unique protein chains: 1

1JL7

Crystal Structure Of CN-Ligated Component III Glycera Dibranchiata Monomeric Hemoglobin

• DOI: 10.2210/pdb1JL7/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Glycera dibranchiata


• Deposited: 2001-07-16 Released: 2002-07-16 
• Deposition Author(s): Park, H.J., Yang, C., Treff, N., Satterlee, J.D., Kang, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.4 Å
• R-Value Free: 0.215 
• R-Value Work: 0.175 

Literature

Crystal Structures of Unligated and CN-Ligated Glycera dibranchiata Monomer Ferric Hemoglobin Components III and IV

Park, H.J., Yang, C., Treff, N., Satterlee, J.D., Kang, C.

(2002) Proteins 49: 49-60

• PubMed: 12211015 
• DOI: 10.1002/prot.10199
• Primary Citation of Related Structures:  
  1JL6, 1JF4, 1JF3


• PubMed Abstract: 
  

Erythrocytes of the marine annelid, Glycera dibranchiata, contain a mixture of monomeric and polymeric hemoglobins. There are three major monomer hemoglobin components, II, III, IV (also called GMH2, 3, and 4), that have been highly purified and well characterized. We have now crystallized GMH3 and GMH4 and determined their structures to 1.4-1.8 A resolution. The structures were determined for these two monomer hemoglobins in the oxidized (Fe3+, ferric, or met-) forms in both the unligated and cyanide-ligated states. This work differs from two published, refined structures of a Glycera dibranchiata monomer hemoglobin, which has a sequence that is substantially different from any bona fide major monomer hemoglobins (GMH2, 3, or 4). The high-resolution crystal structures (presented here) and the previous NMR structure of CO-ligated GMH4, provide a basis for interpreting structure/function details of the monomer hemoglobins. These details include: (1) the strong correlation between temperature factor and NMR dynamics for respective protein forms; (2) the unique nature of the HisE7Leu primary sequence substitutions in GMH3 and GMH4 and their impact on cyanide ion binding kinetics; (3) the LeuB10Phe difference between GMH3 and GMH4 and its impact on ligand binding; and (4) elucidation of changes in the structural details of the distal and proximal heme pockets upon cyanide binding.

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Organizational Affiliation: 

School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Monomer hemoglobin component III	A	147	Glycera dibranchiata	Mutation(s): 0
Find proteins for P02216 (Glycera dibranchiata) Go to UniProtKB:  P02216

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CYN	A	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.4 Å
• R-Value Free: 0.215 
• R-Value Work: 0.175 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 61.454	α = 90.00
b = 32.814	β = 109.99
c = 40.905	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-07-16 
• Released Date: 2002-07-16 
• Deposition Author(s): Park, H.J., Yang, C., Treff, N., Satterlee, J.D., Kang, C.

Revision History 

• Version 1.0: 2002-07-16
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance