1UPM

ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+.

Structural Biology Knowledgebase: 1UPM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.230

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1UPM

Classification: LYASE

Total Structure Weight: 543082.63

Macromolecule Entities
Molecule Chains Length Organism Details
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN B, E, H..., K, L, O, R, VB, E, H, K, L, O, R, V 475 Spinacia oleracea EC#: 4.1.1.39 IUBMB
Gene Name(s): rbcL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN C, F, I..., M, P, S, T, WC, F, I, M, P, S, T, W 123 Spinacia oleracea EC#: 4.1.1.39 IUBMB
Mutation: K2Q, T6I, Q7L, M9L, R11K, Q109E, V113I
Details: THE COMPLETE STRUCTURE HAS BEEN SUBMITTED AS WELL AS THE MATRIX TRANSFORMATION FOR EACH CHAIN.
Gene Name(s): RBCS2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

B, E, H, K, L, O, R, V 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

B, E, H, K, L, O, R, V 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
B, E, H, K, L, O, R, V L-PEPTIDE LINKING C7 H14 N2 O4 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.230
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 219.60 α = 90.00
b = 220.94 β = 90.00
c = 116.98 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-10-08
  • 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