1RBL

STRUCTURE DETERMINATION AND REFINEMENT OF RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM SYNECHOCOCCUS PCC6301


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure determination and refinement of ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301.

Newman, J.Branden, C.I.Jones, T.A.

(1993) Acta Crystallogr D Biol Crystallogr 49: 548-560

  • DOI: https://doi.org/10.1107/S090744499300530X
  • Primary Citation of Related Structures:  
    1RBL

  • PubMed Abstract: 

    The structure of an activated quaternary complex of ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) from Synechococcus PCC6301 has been solved by molecular replacement. The protein crystallizes in an orthorhombic P2(1)2(1)2(1) unit cell with a complete L(8)S(8) complex consisting of 4608 residues (37 680 non-hydrogen atoms) in the asymmetric unit. Data were collected both on film and image plate using synchrotron radiation; there were 218 276 unique reflections in the final 2.2 A data set. The eightfold non-crystallographic symmetry could be used both to improve map quality and to reduce the computing requirements of refinement. The coordinates were refined using strict non-crystallographic symmetry constraints. The stereochemistry of the final model is good, and the model has an R value of 20.0% for the reflections between 7 and 2.2 A.


  • Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Biomedical Centre, Uppsala, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)467Synechococcus elongatus PCC 6301Mutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for P00880 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore P00880 
Go to UniProtKB:  P00880
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00880
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)109Synechococcus elongatus PCC 6301Mutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for P04716 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore P04716 
Go to UniProtKB:  P04716
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04716
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAP
Query on CAP

Download Ideal Coordinates CCD File 
AA [auth D]
DA [auth E]
GA [auth F]
JA [auth G]
MA [auth H]
AA [auth D],
DA [auth E],
GA [auth F],
JA [auth G],
MA [auth H],
R [auth A],
U [auth B],
X [auth C]
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
BA [auth D]
EA [auth E]
HA [auth F]
KA [auth G]
NA [auth H]
BA [auth D],
EA [auth E],
HA [auth F],
KA [auth G],
NA [auth H],
S [auth A],
V [auth B],
Y [auth C]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth E]
FA [auth F]
IA [auth G]
LA [auth H]
Q [auth A]
CA [auth E],
FA [auth F],
IA [auth G],
LA [auth H],
Q [auth A],
T [auth B],
W [auth C],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.9α = 90
b = 111.9β = 90
c = 199.7γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-10
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2024-06-05
    Changes: Data collection, Database references, Derived calculations, Other