5IU0 | pdb_00005iu0

Rubisco from Arabidopsis thaliana

PDB DOI: https://doi.org/10.2210/pdb5IU0/pdb

Classification: LYASE
Organism(s): Arabidopsis thaliana
Mutation(s): No

Deposited: 2016-03-17 Released: 2017-07-12
Deposition Author(s): Valegaard, K., Hasse, D., Gunn, L., Andersson, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.152 (Depositor), 0.152 (DCC)
R-Value Work:
0.136 (Depositor), 0.137 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bisphosphate.

Valegard, K., Hasse, D., Andersson, I., Gunn, L.H.

(2018) Acta Crystallogr D Struct Biol 74: 1-9

PubMed: 29372894 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2059798317017132
Primary Citation Related Structures:
5IU0

PubMed Abstract:
The crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Arabidopsis thaliana is reported at 1.5 Å resolution. In light of the importance of A. thaliana as a model organism for understanding higher plant biology, and the pivotal role of Rubisco in photosynthetic carbon assimilation, there has been a notable absence of an A. thaliana Rubisco crystal structure. A. thaliana Rubisco is an L ₈S ₈ hexadecamer comprising eight plastome-encoded catalytic large (L) subunits and eight nuclear-encoded small (S) subunits. A. thaliana produces four distinct small-subunit isoforms (RbcS1A, RbcS1B, RbcS2B and RbcS3B), and this crystal structure provides a snapshot of A. thaliana Rubisco containing the low-abundance RbcS3B small-subunit isoform. Crystals were obtained in the presence of the transition-state analogue 2-carboxy-D-arabinitol-1,5-bisphosphate. A. thaliana Rubisco shares the overall fold characteristic of higher plant Rubiscos, but exhibits an interesting disparity between sequence and structural relatedness to other Rubisco isoforms. These results provide the structural framework to understand A. thaliana Rubisco and the potential catalytic differences that could be conferred by alternative A. thaliana Rubisco small-subunit isoforms.

Organizational Affiliation

Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden.

Macromolecule Content

Total Structure Weight: 148.31 kDa
Atom Count: 10,407
Modeled Residue Count: 1,172
Deposited Residue Count: 1,320
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase large chain	A, B	479	Arabidopsis thaliana	Mutation(s): 0 EC: 4.1.1.39
UniProt
Find proteins for O03042 (Arabidopsis thaliana) Explore O03042 Go to UniProtKB: O03042
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O03042
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase small chain 1B, chloroplastic	C [auth J], D [auth I]	181	Arabidopsis thaliana	Mutation(s): 0 EC: 4.1.1.39
UniProt
Find proteins for P10796 (Arabidopsis thaliana) Explore P10796 Go to UniProtKB: P10796
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10796
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAP Query on CAP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain P [auth B] mmCIF format, chain F [auth A] mmCIF format, chain P [auth B]	F [auth A], P [auth B]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C₆ H₁₄ O₁₃ P₂ ITHCSGCUQDMYAI-ZMIZWQJLSA-N		Interactions Focus chain F [auth A] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain P [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth I] SDF format, chain U [auth I] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth I] MOL2 format, chain U [auth I] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth I] mmCIF format, chain U [auth I]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth B], T [auth I], U [auth I]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth I] Focus chain U [auth I] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth I] Focus chain U [auth I]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] mmCIF format, chain E [auth A] mmCIF format, chain O [auth B]	E [auth A], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain O [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.152 (Depositor), 0.152 (DCC)
R-Value Work: 0.136 (Depositor), 0.137 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.86	α = 90
b = 111.86	β = 90
c = 197.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-07-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-12
Type: Initial release
Version 1.1: 2018-01-03
Changes: Database references
Version 1.2: 2018-02-07
Changes: Database references
Version 1.3: 2019-10-16
Changes: Data collection
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description