4L2M

Crystal structure of the 2/2 hemoglobin from Synechococcus sp. PCC 7002 in the cyanomet state and with covalently attached heme

• PDB DOI: https://doi.org/10.2210/pdb4L2M/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Picosynechococcus sp. PCC 7002
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-04 Released: 2013-06-12 
• Deposition Author(s): Wenke, B.B., Schlessman, J.L., Heroux, A., Lecomte, J.T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.288 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 

Literature

The 2/2 hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002 with covalently attached heme: Comparison of X-ray and NMR structures.

Wenke, B.B., Lecomte, J.T., Heroux, A., Schlessman, J.L.

(2014) Proteins 82: 528-534

• PubMed: 23999883 
• DOI: https://doi.org/10.1002/prot.24409
• Primary Citation of Related Structures:  
  4L2M, 4MAX


• PubMed Abstract: 
  

  The X-ray structures of the hemoglobin from Synechococcus sp. PCC 7002 (GlbN) were solved in the ferric bis-histidine (1.44 Å resolution) and cyanide-bound (2.25 Å resolution) states with covalently attached heme. The two structures illustrate the conformational changes and cavity opening caused by exogenous ligand binding. They also reveal an unusually distorted heme, ruffled as in c cytochromes. Comparison to the solution structure demonstrates the influence of crystal packing on several structural elements, whereas comparison to GlbN from Synechocystis sp. PCC 6803 shows subtle differences in heme geometries and environment. The new structures will be instrumental in elucidating GlbN reactivity.

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Organizational Affiliation: 

T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, 21218.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.06 kDa 
• Atom Count: 2,076 
• Modelled Residue Count: 246 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyanoglobin	A, B	123	Picosynechococcus sp. PCC 7002	Mutation(s): 0  Gene Names: glbN, SYNPCC7002_A1621
UniProt
Find proteins for Q8RT58 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6)) Explore Q8RT58  Go to UniProtKB:  Q8RT58

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEB	C [auth A], F [auth B]	HEME B/C C34 H34 Fe N4 O4 NEGHHAJBRZGUAY-RGGAHWMASA-L
SO4	E [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CYN	D [auth A], G [auth B]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.288 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.622	α = 90
b = 40.951	β = 111.21
c = 66.461	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-12 
Deposition Author(s): Wenke, B.B., Schlessman, J.L., Heroux, A., Lecomte, J.T.J.

Revision History  

• Version 1.0: 2013-06-12
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Experimental preparation
• Version 1.2: 2013-09-18
  Changes: Database references
• Version 1.3: 2014-02-19
  Changes: Database references
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description