1RCX Lyase (Carbon-Carbon) date Dec 06, 1996
title Non-Activated Spinach Rubisco In Complex With Its Substrate Ribulose-1,5-Bisphosphate
authors T.C.Taylor, I.Andersson
compound source
Molecule: Ribulose Bisphosphate Carboxylaseoxygenase
Chain: L, B, E, H, K, O, R, V
Synonym: Rubisco
Ec: 4.1.1.39
Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562
Organ: Leaf

Molecule: Ribulose Bisphosphate Carboxylaseoxygenase
Chain: S, C, F, I, M, P, T, W
Synonym: Rubisco
Ec: 4.1.1.39

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562
Organ: Leaf
symmetry Space Group: P 21 21 2
R_factor 0.224 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
218.300 219.000 113.500 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand RUB enzyme Lyase E.C.4.1.1.39 BRENDA
note 1RCX (Molecule of the Month:pdb11)
related structures by homologous chain: 1EJ7, 1UZD
Gene
Ontology
ChainFunctionProcessComponent
K, E, V, L, O, B, H, R


S, F, T, M, C, W, P, I


Primary referenceThe structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate., Taylor TC, Andersson I, J Mol Biol 1997 Jan 31;265(4):432-44. PMID:9034362
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (791 Kb) [Save to disk]
  • Biological Unit Coordinates (1rcx.pdb1.gz) 785 Kb
  • LPC: Ligand-Protein Contacts for 1RCX
  • CSU: Contacts of Structural Units for 1RCX
  • Likely Quarternary Molecular Structure file(s) for 1RCX
  • Structure Factors (1187 Kb)
  • Retrieve 1RCX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RCX from S2C, [Save to disk]
  • Re-refined 1rcx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RCX 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 1RCX
  • 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 1RCX, from MSDmotif at EBI
  • Genome occurence of 1RCX's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rcxb1, region B:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxb2, region B:9-147 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1rcxe1, region E:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxe2, region E:9-147 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1rcxh1, region H:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxh2, region H:9-147 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1rcxk1, region K:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxk2, region K:9-147 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxl1, region L:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxl2, region L:9-147 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxm_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1rcxo1, region O:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxo2, region O:9-147 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxp_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1rcxr1, region R:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxr2, region R:9-147 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxs_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1rcxt_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1rcxv1, region V:148-475 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxv2, region V:9-147 [Jmol] [rasmolscript] [script source]
        - Domain d1rcxw_, region W [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: [1rcx_T] [1rcx_K] [1rcx_F] [1rcx_M] [1rcx_O] [1rcx_P] [1rcx_I] [1rcx_H] [1rcx] [1rcx_S] [1rcx_R] [1rcx_V] [1rcx_C] [1rcx_B] [1rcx_L] [1rcx_E] [1rcx_W]
  • SWISS-PROT database: [P00875] [P00870]
  • Domain organization of [RBL_SPIOL] [RBS1_SPIOL] by SWISSPFAM
  • Domain found in 1RCX: [RuBisCO_small ] by SMART
  • Other resources with information on 1RCX
  • Community annotation for 1RCX 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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