1E29 | pdb_00001e29

PSII associated cytochrome C549 from Synechocystis sp.

• PDB DOI: https://doi.org/10.2210/pdb1E29/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Synechocystis sp.
• Mutation(s): No 


• Deposited: 2000-05-19 Released: 2001-05-04 
• Deposition Author(s): Frazao, C., Enguita, F.J., Coelho, R., Sheldrick, G.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 
  0.212 (Depositor) 
• R-Value Work: 
  0.151 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Literature

Crystal Structure of Low-Potential Cytochrome C549 from Synechocystis Sp. Pcc 6803 at 1.21A Resolution

Frazao, C., Enguita, F.J., Coelho, R., Sheldrick, G.M., Navarro, J.A., Hervas, M., De La Rosa, M.A., Carrondo, M.A.

(2001) J Biol Inorg Chem 6: 324

• PubMed: 11315568 
• DOI: https://doi.org/10.1007/s007750100208
• Primary Citation of Related Structures:  
  1E29


• PubMed Abstract: 
  

  The crystal structure of low-potential cytochrome c549, an extrinsic component of the photosystem II (PS II) from Synechocystis sp. PCC 6803, was obtained directly from single-wavelength 1.21 A resolution diffraction data. This is the first monodomain bis-histidinyl monoheme cytochrome c to be structurally characterized. The extended N-terminal region of c549 builds up a two-strand antiparallel beta-sheet in a hairpin motif, which extends through two molecules owing to crystal packing. Both peptide termini are involved in crystal contacts, which may explain their protrusion out of the globular fold. The C-terminus is preceded by a 9 A-long hydrophobic finger extending from a positively charged base and could be involved in PSII interactions, as well as a protruding negative patch built by a set of conserved acidic residues among c549 sequences.

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Organizational Affiliation: 

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal.

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 15.87 kDa 
• Atom Count: 1,342 
• Modelled Residue Count: 135 
• Deposited Residue Count: 135 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C549	A	135	Synechocystis sp.	Mutation(s): 0
UniProt
Find proteins for Q55013 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55013  Go to UniProtKB:  Q55013

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	B [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
CA	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free:  0.212 (Depositor) 
• R-Value Work:  0.151 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.22	α = 90
b = 86.86	β = 90
c = 97.66	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-05-04 
Deposition Author(s): Frazao, C., Enguita, F.J., Coelho, R., Sheldrick, G.M.

Revision History  

• Version 1.0: 2001-05-04
  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: 2017-07-12
  Changes: Derived calculations
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.5: 2019-05-22
  Changes: Data collection, Refinement description
• Version 1.6: 2019-07-24
  Changes: Data collection
• Version 1.7: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary