7T1J

Crystal structure of RUBISCO from Rhodospirillaceae bacterium BRH_c57


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural plasticity enables evolution and innovation of RuBisCO assemblies.

Liu, A.K.Pereira, J.H.Kehl, A.J.Rosenberg, D.J.Orr, D.J.Chu, S.K.S.Banda, D.M.Hammel, M.Adams, P.D.Siegel, J.B.Shih, P.M.

(2022) Sci Adv 8: eadc9440-eadc9440

  • DOI: https://doi.org/10.1126/sciadv.adc9440
  • Primary Citation of Related Structures:  
    7T1C, 7T1J

  • PubMed Abstract: 

    Oligomerization is a core structural feature that defines the form and function of many proteins. Most proteins form molecular complexes; however, there remains a dearth of diversity-driven structural studies investigating the evolutionary trajectory of these assemblies. Ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is one such enzyme that adopts multiple assemblies, although the origins and distribution of its different oligomeric states remain cryptic. Here, we retrace the evolution of ancestral and extant form II RuBisCOs, revealing a complex and diverse history of oligomerization. We structurally characterize a newly discovered tetrameric RuBisCO, elucidating how solvent-exposed surfaces can readily adopt new interactions to interconvert or give rise to new oligomeric states. We further use these principles to engineer and demonstrate how changes in oligomerization can be mediated by relatively few mutations. Our findings yield insight into how structural plasticity may give rise to new oligomeric states.


  • Organizational Affiliation

    Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
460Rhodospirillaceae bacterium BRH_c57Mutation(s): 0 
Gene Names: cbbMVR70_18855
EC: 4.1.1.39
UniProt
Find proteins for A0A0F2R9T6 (Rhodospirillaceae bacterium BRH_c57)
Explore A0A0F2R9T6 
Go to UniProtKB:  A0A0F2R9T6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F2R9T6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAP (Subject of Investigation/LOI)
Query on CAP

Download Ideal Coordinates CCD File 
AA [auth H]
CA [auth I]
EA [auth J]
GA [auth K]
IA [auth L]
AA [auth H],
CA [auth I],
EA [auth J],
GA [auth K],
IA [auth L],
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
W [auth F],
Y [auth G]
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth H]
DA [auth I]
FA [auth J]
HA [auth K]
JA [auth L]
BA [auth H],
DA [auth I],
FA [auth J],
HA [auth K],
JA [auth L],
N [auth A],
P [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F],
Z [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.807α = 90
b = 104.978β = 93.04
c = 369.611γ = 90
Software Package:
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-15
    Changes: Data collection