1IR2 Lyase date Sep 03, 2001
title Crystal Structure Of Activated Ribulose-1,5-Bisphosphate Carboxylaseoxygenase (Rubisco) From Green Alga, Chlamydomo Reinhardtii Complexed With 2-Carboxyarabinitol-1,5-Bisphosp Cabp)
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, E, F, G, H, S, T, U, V, W, X, Y, Z
Synonym: Ribulose Bisphosphate Carboxylase Large Chain
Ec: 4.1.1.39
 Organism_scientific: Chlamydomonas Reinhardtii
Organism_taxid: 3055
Strain: 137c Mt+

Molecule: Small Subunit Of Rubisco
Chain: I, J, K, L, M, N, O, P, 1, 2, 3, 4, 5, 6, 7, 8
Synonym: Ribulose Bisphosphate Carboxylase Small Chain 2
Ec: 4.1.1.39
Organism_scientific: Chlamydomonas Reinhardtii
Organism_taxid: 3055
Strain: 137c Mt+
symmetry Space Group: P 1 21 1
R_factor 0.152 R_Free 0.181
crystal
cell
length a length b length c angle alpha angle beta angle gamma
129.170 174.750 222.270 90.00 97.75 90.00
method X-Ray Diffractionresolution 1.84 Å
ligand CAP, GOL, HYP, KCX, MG, MME, SMC enzyme Lyase E.C.4.1.1.39 BRENDA
related structures by homologous chain: 1GK8, 1IR1, 1UW9, 3RUB
Gene
Ontology
ChainFunctionProcessComponent
S, F, T, Y, E, V, Z, C, A, W, X, B, H, D, G, U


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] (1717 Kb) [Save to disk]
  • Biological Unit Coordinates (1ir2.pdb1.gz) 860 Kb
  • Biological Unit Coordinates (1ir2.pdb2.gz) 859 Kb
  • LPC: Ligand-Protein Contacts for 1IR2
  • CSU: Contacts of Structural Units for 1IR2
  • Likely Quarternary Molecular Structure file(s) for 1IR2
  • Structure Factors (7170 Kb)
  • Retrieve 1IR2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IR2 from S2C, [Save to disk]
  • Re-refined 1ir2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1IR2 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 1IR2
  • 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
  • 3D motif for 1IR2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ir21_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1ir22_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1ir23_, region 3 [Jmol] [rasmolscript] [script source]
        - Domain d1ir24_, region 4 [Jmol] [rasmolscript] [script source]
        - Domain d1ir25_, region 5 [Jmol] [rasmolscript] [script source]
        - Domain d1ir26_, region 6 [Jmol] [rasmolscript] [script source]
        - Domain d1ir27_, region 7 [Jmol] [rasmolscript] [script source]
        - Domain d1ir28_, region 8 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2a1, region A:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2a2, region A:8-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2b1, region B:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2b2, region B:9-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2c2, region C:10-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2c1, region C:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2d1, region D:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2d2, region D:9-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2e2, region E:11-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2e1, region E:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2f2, region F:11-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2f1, region F:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2g2, region G:10-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2g1, region G:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2h1, region H:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2h2, region H:8-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1ir2j_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1ir2k_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1ir2l_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1ir2m_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1ir2n_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1ir2o_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1ir2p_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1ir2s2, region S:11-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2s1, region S:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2t2, region T:10-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2t1, region T:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2u1, region U:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2u2, region U:7-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2v1, region V:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2v2, region V:7-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2w2, region W:10-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2w1, region W:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2x2, region X:10-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2x1, region X:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2y2, region Y:11-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2y1, region Y:150-475 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2z2, region Z:10-149 [Jmol] [rasmolscript] [script source]
        - Domain d1ir2z1, region Z:150-475 [Jmol] [rasmolscript] [script source]
  • 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: [1ir2_D] [1ir2_4] [1ir2_7] [1ir2_B] [1ir2_I] [1ir2_K] [1ir2_P] [1ir2_6] [1ir2_C] [1ir2_S] [1ir2_H] [1ir2_2] [1ir2_F] [1ir2_1] [1ir2_Y] [1ir2_U] [1ir2_T] [1ir2_3] [1ir2_X] [1ir2_Z] [1ir2_O] [1ir2_W] [1ir2_M] [1ir2_N] [1ir2_V] [1ir2_E] [1ir2_8] [1ir2_L] [1ir2_5] [1ir2_G] [1ir2] [1ir2_J] [1ir2_A]
  • SWISS-PROT database: [P00877] [P08475]
  • Domain organization of [RBL_CHLRE] [RBS2_CHLRE] by SWISSPFAM
  • Domain found in 1IR2: [RuBisCO_small ] by SMART
    • Other resources with information on 1IR2
  • Community annotation for 1IR2 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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