6KQ1

Crystal structure of cytochrome c551 from Pseudomonas sp. strain MT-1.

• PDB DOI: https://doi.org/10.2210/pdb6KQ1/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Pseudomonas sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-16 Released: 2020-08-19 
• Deposition Author(s): Fujii, S., Oki, H., Kawahara, K., Ohkubo, T., Masanari-Fujii, M., Wakai, S., Sambongi, Y.
• Funding Organization(s): Japan Society for the Promotion of Science, Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.224 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

Structural insights into high stability of cytochrome c551 from a deep-sea piezo-tolerant bacterium, Pseudomonas sp. strain MT-1

Fujii, S., Oki, H., Kawahara, K., Ohkubo, T., Masanari-Fujii, M., Wakai, S., Sambongi, Y.

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)

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: 18.78 kDa 
• Atom Count: 1,506 
• Modelled Residue Count: 164 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome C biogenesis protein CcsA	A, B	82	Pseudomonas sp.	Mutation(s): 0  Gene Names: CMK99_21520, CML01_09540, DD989_05085

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC (Subject of Investigation/LOI)	E [auth A], I [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
ZN	C [auth A], D [auth A], F [auth B], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.224 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.787	α = 90
b = 52.017	β = 90
c = 62.393	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Fujii, S., Oki, H., Kawahara, K., Ohkubo, T., Masanari-Fujii, M., Wakai, S., Sambongi, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	25-1446
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	26240045

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description