5Z49

Crystal structure of the effector-binding domain of Synechococcus elongatus CmpR in complex with ribulose-1,5-bisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Literature

Crystal structure of the effector-binding domain of Synechococcus elongatus CmpR in complex with ribulose 1,5-bisphosphate.

Mahounga, D.M.Sun, H.Jiang, Y.L.

(2018) Acta Crystallogr F Struct Biol Commun 74: 506-511

  • DOI: https://doi.org/10.1107/S2053230X18008841
  • Primary Citation of Related Structures:  
    5Z49

  • PubMed Abstract: 

    The CO 2 -concentrating mechanism (CCM) has evolved to improve the efficiency of photosynthesis in autotrophic cyanobacteria. CmpR, a LysR-type transcriptional regulator (LTTR) from Synechococcus elongatus PCC 7942, was found to regulate CCM-related genes under low-CO 2 conditions. Here, the dimeric structure of the effector-binding domain of CmpR (CmpR-EBD) in complex with the co-activator ribulose 1,5-bisphosphate (RuBP) is reported at 2.15 Å resolution. One RuBP molecule binds to the inter-domain cleft between the two subunits of the CmpR-EBD dimer. Structural comparison combined with sequence analyses demonstrated that CmpR-EBD has an overall structure similar to those of LTTRs of known structure, but possesses a distinctly different effector-binding pattern.


  • Organizational Affiliation

    School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HTH-type transcriptional activator CmpRA [auth B],
B [auth A]
239Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: cmpRSynpcc7942_1310
UniProt
Find proteins for Q9F1R2 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q9F1R2 
Go to UniProtKB:  Q9F1R2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F1R2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RUB
Query on RUB

Download Ideal Coordinates CCD File 
C [auth A]RIBULOSE-1,5-DIPHOSPHATE
C5 H12 O11 P2
YAHZABJORDUQGO-NQXXGFSBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.57α = 90
b = 86.7β = 90
c = 87.18γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31630001
National Natural Science Foundation of ChinaChina31500598

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary