Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.72 kDa 
• Atom Count: 1175 
• Modelled Residue Count: 123 
• Deposited Residue Count: 124 
• Unique protein chains: 1

1S69

The X-ray structure of the cyanobacteria Synechocystis hemoglobin "cyanoglobin" with cyanide ligand

• PDB DOI: 10.2210/pdb1S69/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Synechocystis sp. PCC 6803
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-01-22 Released: 2004-09-21 
• Deposition Author(s): Trent III, J.T., Kundu, S., Hoy, J.A., Hargrove, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.199 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

Crystallographic analysis of synechocystis cyanoglobin reveals the structural changes accompanying ligand binding in a hexacoordinate hemoglobin.

Trent III, J.T., Kundu, S., Hoy, J.A., Hargrove, M.S.

(2004) J Mol Biol 341: 1097-1108

• PubMed: 15289104 
• DOI: 10.1016/j.jmb.2004.05.070
• Primary Citation of Related Structures:  
  1S69, 1S6A


• PubMed Abstract: 
  

The crystal structures of cyanide and azide-bound forms of the truncated hemoglobin from Synechocystis are presented at 1.8 angstroms resolution. A comparison with the structure of the endogenously liganded protein reveals a conformational shift unprecedented in hemoglobins, and provides the first picture of a hexacoordinate hemoglobin in both the bis-histidyl and the exogenously coordinated states. The structural changes between the different conformations are confined to two regions of the protein; the B helix, and the E helix, including the EF loop. A molecular "hinge" controlling movement of the E helix is observed in the EF loop, which is composed of three principal structural elements: Arg64, the heme-d-propionate, and a three-residue extension of the F helix. Additional features of the structural transition between the two protein conformations are discussed as they relate to the complex ligand-binding behavior observed in hexacoordinate hemoglobins, and the potential physiological function of this class of proteins.

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Organizational Affiliation: 

Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50010, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyanoglobin	A	124	Synechocystis sp. PCC 6803	Mutation(s): 0  Gene Names: glbN, slr2097
UniProt
Find proteins for P73925 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P73925  Go to UniProtKB:  P73925

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
FLC	B [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
CYN	C [auth A]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.199 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.06	α = 90
b = 84.06	β = 90
c = 64.62	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CRYSTAL	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-01-22 
• Released Date: 2004-09-21 
Deposition Author(s): Trent III, J.T., Kundu, S., Hoy, J.A., Hargrove, M.S.

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance