Biological Assembly 1  

 3D View: Structure | 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: 16.76 kDa 
• Atom Count: 1256 
• Modelled Residue Count: 131 
• Deposited Residue Count: 137 
• Unique protein chains: 1

1MZ4

Crystal Structure of Cytochrome c550 from Thermosynechococcus elongatus

• DOI: 10.2210/pdb1MZ4/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Thermosynechococcus vestitus
• Mutation(s): No 


• Deposited: 2002-10-05 Released: 2003-09-23 
• Deposition Author(s): Kerfeld, C.A., Sawaya, M.R., Bottin, H., Tran, K.T., Sugiura, M., Kirilovsky, D., Krogmann, D., Yeates, T.O., Boussac, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.202 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 

Literature

Structural and EPR characterization of the soluble form of cytochrome c-550 and of the psbV2 gene product from the cyanobacterium Thermosynechococcus elongatus.

Kerfeld, C.A., Sawaya, M.R., Bottin, H., Tran, K.T., Sugiura, M., Cascio, D., Desbois, A., Yeates, T.O., Kirilovsky, D., Boussac, A.

(2003) Plant Cell Physiol 44: 697-706

• PubMed: 12881497 
• DOI: 10.1093/pcp/pcg084
• Primary Citation of Related Structures:  
  1MZ4


• PubMed Abstract: 
  

First, the crystal structure of cytochrome c-550 (the psbV1 gene product) from the thermophilic cyanobacterium Thermosynechococcus elongatus has been determined to a resolution of 1.8 A. A comparison of the T. elongatus cytochrome c-550 structure to its counterparts from mesophilic organisms, Synechocystis 6803 and Arthrospira maxima, suggests that increased numbers of hydrogen bonds may play a role in the structural basis of thermostability. The cytochrome c-550 in T. elongatus also differs from that in Synechocystis 6803 and Arthrospira maxima in its lack of dimerization and the presence of a trigonal planar molecule, possibly bicarbonate, tightly bound to the heme propionate oxygen atoms. Cytochromes c-550 from T. elongatus, Synechocystis 6803 and Arthrospira maxima exhibit different EPR spectra. A correlation has been done between the heme-axial ligands geometries and the rhombicity calculated from the EPR spectra. This correlation indicates that binding of cytochrome c-550 to Photosystem II is accompanied by structural changes in the heme vicinity. Second, the psbV2 gene product has been found and purified. The UV-visible, EPR and Raman spectra are reported. From the spectroscopic data and from a theoretical structural model based on the cytochrome c-550 structure it is proposed that the 6th ligand of the heme-iron is the Tyr86.

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Organizational Affiliation: 

Molecular Biology Institute, UCLA, Box 951570, Los Angeles, CA 90095-1570, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cytochrome c550	A	137	Thermosynechococcus vestitus	Mutation(s): 0
UniProt
Find proteins for P0A386 (Thermosynechococcus elongatus (strain BP-1)) Explore P0A386  Go to UniProtKB:  P0A386

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC (Subject of Investigation/LOI)	H [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
PO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT	G [auth A]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.202 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.641	α = 90
b = 69.641	β = 90
c = 92.849	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2002-10-05 
• Released Date: 2003-09-23 
Deposition Author(s): Kerfeld, C.A., Sawaya, M.R., Bottin, H., Tran, K.T., Sugiura, M., Kirilovsky, D., Krogmann, D., Yeates, T.O., Boussac, A.

Revision History  

• Version 1.0: 2003-09-23
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2021-03-03
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary