8RUC Lyase (Carbon-Carbon) date Feb 22, 1996
title Activated Spinach Rubisco Complexed With 2-Carboxyarabinitol Bisphosphate
authors I.Andersson, S.Knight, C.I.Branden
compound source
Molecule: Ribulose-1,5-Bisphosphate Carboxylaseoxygenase
Chain: A, C, E, G
Synonym: Rubisco
Ec: 4.1.1.39
Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562
Organ: Leaf

Molecule: Ribulose-1,5-Bisphosphate Carboxylaseoxygenase
Chain: I, J, K, L
Synonym: Rubisco
Ec: 4.1.1.39

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562
Organ: Leaf
symmetry Space Group: C 2 2 21
R_factor 0.211 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
157.200 157.200 201.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand CAP, KCX, MG enzyme Lyase E.C.4.1.1.39 BRENDA
note 8RUC (Molecule of the Month:pdb11)supersedes 8RUB
related structures by homologous chain: 1GK8, 1IR1, 1SVD, 1WDD
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, G


J, K, I, L


Primary referenceLarge structures at high resolution: the 1.6 A crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate., Andersson I, J Mol Biol 1996 May 31;259(1):160-74. PMID:8648644
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (411 Kb) [Save to disk]
  • Biological Unit Coordinates (8ruc.pdb1.gz) 806 Kb
  • LPC: Ligand-Protein Contacts for 8RUC
  • CSU: Contacts of Structural Units for 8RUC
  • Likely Quarternary Molecular Structure file(s) for 8RUC
  • Structure Factors (1749 Kb)
  • Retrieve 8RUC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 8RUC from S2C, [Save to disk]
  • Re-refined 8ruc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 8RUC in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 8RUC
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 8RUC, from MSDmotif at EBI
  • Genome occurence of 8RUC's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d8ruca1, region A:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d8ruca2, region A:9-147 [Jmol] [rasmolscript] [script source]
        - Domain d8rucc1, region C:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d8rucc2, region C:9-147 [Jmol] [rasmolscript] [script source]
        - Domain d8ruce1, region E:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d8ruce2, region E:9-147 [Jmol] [rasmolscript] [script source]
        - Domain d8rucg1, region G:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d8rucg2, region G:9-147 [Jmol] [rasmolscript] [script source]
        - Domain d8ruci_, region I [Jmol] [rasmolscript] [script source]
        - Domain d8rucj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d8ruck_, region K [Jmol] [rasmolscript] [script source]
        - Domain d8rucl_, region L [Jmol] [rasmolscript] [script source]
  • Fold representative 8ruc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [8ruc_L] [8ruc_I] [8ruc_J] [8ruc] [8ruc_A] [8ruc_K] [8ruc_C] [8ruc_G] [8ruc_E]
  • SWISS-PROT database: [P00875] [P00870]
  • Domain organization of [RBL_SPIOL] [RBS1_SPIOL] by SWISSPFAM
  • Domain found in 8RUC: [RuBisCO_small ] by SMART
  • Other resources with information on 8RUC
  • Community annotation for 8RUC at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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