3ZXW

STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure of Ribulose-1,5-Bisphosphate Carboxylase Oxygenase from Thermosynechococcus Elongatus

Terlecka, B.Wilhelmi, V.Bialek, W.Gubernator, B.Szczepaniak, A.Hofmann, E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAINA, C, E, G475Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: cbbLrbcLtll1506
EC: 4.1.1.39
UniProt
Find proteins for Q8DIS5 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
Explore Q8DIS5 
Go to UniProtKB:  Q8DIS5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIS5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAINB, D, F, H118Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: cbbSrbcStll1504
EC: 4.1.1.39
UniProt
Find proteins for Q8DIS7 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
Explore Q8DIS7 
Go to UniProtKB:  Q8DIS7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIS7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAP
Query on CAP

Download Ideal Coordinates CCD File 
J [auth A],
P [auth C],
V [auth E],
Z [auth G]
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth G],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
AA [auth G],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
W [auth E],
X [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
O [auth C],
U [auth E],
Y [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, C, E, G L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.5α = 90
b = 111.5β = 90
c = 397γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Derived calculations