1IR1 Lyase date Aug 31, 2001
title Crystal Structure Of Spinach Ribulose-1,5-Bisphosphate Carboxylaseoxygenase (Rubisco) Complexed With Co2, Mg2+ An Carboxyarabinitol-1,5-Bisphosphate
authors E.Mizohata, H.Matsumura, Y.Okano, M.Kumei, H.Takuma, J.Onodera, K. N.Shibata, T.Inoue, A.Yokota, Y.Kai
compound source
Molecule: Large Subunit Of Rubisco
Chain: A, B, C, D
Synonym: Ribulose Bisphosphate Carboxylase Large Chain
Ec: 4.1.1.39
Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562
Organ: Leaves

Molecule: Small Subunit Of Rubisco
Chain: S, T, U, V
Synonym: Ribulose Bisphosphate Carboxylase Small Chain 2
Ec: 4.1.1.39

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562
Organ: Leaves
symmetry Space Group: C 2 2 21
R_factor 0.155 R_Free 0.179
crystal
cell
length a length b length c angle alpha angle beta angle gamma
157.800 157.800 200.900 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CAP, KCX, MG, MME enzyme Lyase E.C.4.1.1.39 BRENDA
note 1IR1 supersedes 1BUR
related structures by homologous chain: 1IR2, 1SVD, 3RUB, 8RUC
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceCrystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate., Mizohata E, Matsumura H, Okano Y, Kumei M, Takuma H, Onodera J, Kato K, Shibata N, Inoue T, Yokota A, Kai Y, J Mol Biol 2002 Feb 22;316(3):679-91. PMID:11866526
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (427 Kb) [Save to disk]
  • Biological Unit Coordinates (1ir1.pdb1.gz) 834 Kb
  • LPC: Ligand-Protein Contacts for 1IR1
  • CSU: Contacts of Structural Units for 1IR1
  • Likely Quarternary Molecular Structure file(s) for 1IR1
  • Structure Factors (1734 Kb)
  • Retrieve 1IR1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IR1 from S2C, [Save to disk]
  • Re-refined 1ir1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1IR1 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 1IR1
  • 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 1IR1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ir1a2, region A:12-147 [Jmol] [rasmolscript] [script source]
        - Domain d1ir1a1, region A:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir1b2, region B:12-147 [Jmol] [rasmolscript] [script source]
        - Domain d1ir1b1, region B:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir1c2, region C:12-147 [Jmol] [rasmolscript] [script source]
        - Domain d1ir1c1, region C:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir1d2, region D:12-147 [Jmol] [rasmolscript] [script source]
        - Domain d1ir1d1, region D:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir1s_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1ir1t_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1ir1u_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1ir1v_, region V [Jmol] [rasmolscript] [script source]
  • Fold representative 1ir1 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: [1ir1_B] [1ir1_S] [1ir1_V] [1ir1_A] [1ir1_D] [1ir1] [1ir1_U] [1ir1_T] [1ir1_C]
  • SWISS-PROT database: [P00875] [Q43832]
  • Domain organization of [RBL_SPIOL] [RBS2_SPIOL] by SWISSPFAM
  • Domain found in 1IR1: [RuBisCO_small ] by SMART
  • Other resources with information on 1IR1
  • Community annotation for 1IR1 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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