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 Diffraction	resolution	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	Chain Function Process Component A, D, C, B magnesium ion binding monooxygenase activity oxidoreductase activity lyase activity ribulose-bisphosphate carbox... metal ion binding photorespiration carbon fixation photosynthesis reductive pentose-phosphate ... oxidation-reduction process chloroplast plastid
Primary reference	Crystal 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [1ir1_B] [1ir1_C] [1ir1_D] [1ir1_S] [1ir1_T] [1ir1_U] [1ir1_V] SWISS-PROT database: [P00875] [Q43832] Domain organization of [RBL_SPIOL] [RBS2_SPIOL] by SWISSPFAM Domain found in 1IR1: [RuBisCO_small ] by SMART Alignments of the sequence of 1IR1 with the sequences similar proteins can be viewed for 1IR1's classification [RBL_SPIOL] [RBS2_SPIOL] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [RBL_SPIOL] [RBS2_SPIOL] at ProtoMap. Click on the Cluster number.

Other resources with information on 1IR1

Community annotation for 1IR1 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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