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: 14.73 kDa 
• Atom Count: 1099 
• Modelled Residue Count: 123 
• Deposited Residue Count: 123 
• Unique protein chains: 1

1RTX

Crystal Structure of Synechocystis Hemoglobin with a Covalent Heme Linkage

• PDB DOI: 10.2210/pdb1RTX/pdb

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


• Deposited: 2003-12-10 Released: 2004-04-20 
• Deposition Author(s): Hoy, J.A., Kundu, S., Trent, J.T., Ramaswamy, S., Hargrove, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.224 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

The crystal structure of synechocystis hemoglobin with a covalent heme linkage.

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

(2004) J Biol Chem 279: 16535-16542

• PubMed: 14736872 
• DOI: 10.1074/jbc.M313707200
• Primary Citation of Related Structures:  
  1RTX


• PubMed Abstract: 
  

The x-ray crystal structure of Synechocystis hemoglobin has been solved to a resolution of 1.8 A. The conformation of this structure is surprisingly different from that of the previously reported solution structure, probably due in part to a covalent linkage between the heme 2-vinyl and His117 that is present in the crystal structure but not in the structure solved by NMR. Synechocystis hemoglobin is a hexacoordinate hemoglobin in which the heme iron is coordinated by both the proximal and distal histidines. It is also a member of the "truncated hemoglobin" family that is much shorter in primary structure than vertebrate and plant hemoglobins. In contrast to other truncated hemoglobins, the crystal structure of Synechocystis hemoglobin displays no "ligand tunnel" and shows that several important amino acid side chains extrude into the solvent instead of residing inside the heme pocket. The stereochemistry of hexacoordination is compared with other hexacoordinate hemoglobins and cytochromes in an effort to illuminate factors contributing to ligand affinity in hexacoordinate hemoglobins.

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Organizational Affiliation: 

Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyanoglobin	A	123	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	F [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CD	B [auth A], C [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
K	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.224 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.5	α = 90
b = 46	β = 90
c = 61	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
REFMAC	refinement
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-10 
• Released Date: 2004-04-20 
Deposition Author(s): Hoy, J.A., Kundu, S., Trent, J.T., Ramaswamy, S., Hargrove, M.S.

Revision History  

• Version 1.0: 2004-04-20
  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