9IV3 | pdb_00009iv3

Crystal structure of CcmS-CcmK1 complex from Synechocystis sp. PCC 6803

• PDB DOI: https://doi.org/10.2210/pdb9IV3/pdb

• Classification: CHAPERONE
• Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-22 Released: 2025-03-12 
• Deposition Author(s): Li, J., Deng, J.X., Jiang, Y.L., Zhou, C.Z.
• Funding Organization(s): Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC), Anhui Provincial Key Research and Development Project, Chaohu Lake Biological Resource Investigation and Research Project, USTC Research Funds of the Double First-Class Initiative, Youth Innovation Promotion Association of the Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.278 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Assembly mechanism of beta-carboxysome shell mediated by the chaperone CcmS

Li, J., Deng, J.X., Chen, X., Li, B., Li, B.R., Zhu, Z.L., Liu, J.X., Zhou, C.Z., Jiang, Y.L., Chen, Y.X., Mi, H.L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A6B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 112.35 kDa 
• Atom Count: 6,605 
• Modelled Residue Count: 848 
• Deposited Residue Count: 1,010 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxysome shell protein CcmK1	A, B, C, D, E, F	123	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: ccmK1, sll1029
UniProt
Find proteins for P72760 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P72760  Go to UniProtKB:  P72760

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Slr1911 protein	G, H	136	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: slr1911
UniProt
Find proteins for P73106 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P73106  Go to UniProtKB:  P73106

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.278 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.284	α = 90
b = 129.576	β = 110.44
c = 78.272	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Li, J., Deng, J.X., Jiang, Y.L., Zhou, C.Z.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDA24020302
National Natural Science Foundation of China (NSFC)	China	32171198
National Natural Science Foundation of China (NSFC)	China	32241025
Anhui Provincial Key Research and Development Project	China	2022l07020034
Chaohu Lake Biological Resource Investigation and Research Project	China	2020-340181-77-01-037328
USTC Research Funds of the Double First-Class Initiative	China	YD9100002023
Youth Innovation Promotion Association of the Chinese Academy of Sciences	China	2020452

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release