4EIF

Crystal structure of cytochrome c6C L50Q mutant from Synechococcus sp. PCC 7002

• PDB DOI: https://doi.org/10.2210/pdb4EIF/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Picosynechococcus sp. PCC 7002
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): Yes 


• Deposited: 2012-04-05 Released: 2013-04-10 
• Deposition Author(s): Krzywda, S., Bialek, W., Zatwarnicki, P., Jaskolski, M., Szczepaniak, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 
  0.145 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.119 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.120 (Depositor) 

Starting Model: experimental

Literature

Cytochrome c6 and c6C from Synechococcus sp. PCC 7002 - structure and function.

Bialek, W., Krzywda, S., Zatwarnicki, P., Jaskolski, M., Szczepaniak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 10.26 kDa 
• Atom Count: 879 
• Modelled Residue Count: 82 
• Deposited Residue Count: 87 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c6	A	87	Picosynechococcus sp. PCC 7002	Mutation(s): 1  Gene Names: petJ, petJ2, SYNPCC7002_A2391
UniProt
Find proteins for Q8KX15 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6)) Explore Q8KX15  Go to UniProtKB:  Q8KX15

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	B [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
CL	F [auth A], G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free:  0.145 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.119 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.120 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.38	α = 90
b = 56.38	β = 90
c = 50.05	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-10 
Deposition Author(s): Krzywda, S., Bialek, W., Zatwarnicki, P., Jaskolski, M., Szczepaniak, A.

Revision History  

• Version 1.0: 2013-04-10
  Type: Initial release
  
• Version 2.0: 2021-03-10
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-13
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 2.2: 2024-10-30
  Changes: Structure summary