1UPP

SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE AND CALCIUM.

Structural Biology Knowledgebase: 1UPP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.307
  • R-Value Work: 0.256

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1UPP

Classification: LYASE

Total Structure Weight: 271541.31

Macromolecule Entities
Molecule Chains Length Organism Details
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN A, C, E, G 475 Spinacia oleracea EC#: 4.1.1.39 IUBMB
Gene Name(s): rbcL
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN I, J, K, L 123 Spinacia oleracea EC#: 4.1.1.39 IUBMB
Mutation: K2Q, T6I, Q7L, M9L, R11K, Q109E, V113I
Details: THIS IS THE SECOND STRUCTURE OF THIS COMPLEX THAT IS BEING SUBMITTED. THE PREVOUS STRUCTURE, PDB ID CODE 1UPM, WAS OBTAINED FROM A CRYSTAL OF RUBISCO-CA COOCRYSTALLIZED WITH 2-CABP WHERAS THIS STRUCTURE IS FROM A RUBISCO-CA/3PGA CRYSTAL WHICH WAS SOAKED WITH 2-CABP
Gene Name(s): RBCS2

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CAP
Query on CAP

A, C, E, G 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, C, E, G CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
KCX
Query on KCX
A, C, E, G L-PEPTIDE LINKING C7 H14 N2 O4 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.307
  • R-Value Work: 0.256
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 155.88 α = 90.00
b = 156.25 β = 90.00
c = 199.75 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-10-09
  • Released Date: 2003-10-14
  • Deposition author(s): Karkehabadi, S., Taylor, T.C., Andersson, I.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4