9CQ5 | pdb_00009cq5

Mn-bound RuBisCO from spinach with CABP inhibitor

PDB DOI: https://doi.org/10.2210/pdb9CQ5/pdb

Classification: PLANT PROTEIN
Organism(s): Spinacia oleracea
Mutation(s): No

Deposited: 2024-07-19 Released: 2025-02-05
Deposition Author(s): Voland, R.W., Lancaster, K.M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.242 (Depositor), 0.242 (DCC)
R-Value Work:
0.197 (Depositor), 0.198 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The structure of Mn(II)-bound Rubisco from Spinacia oleracea.

Voland, R.W., Coleman, R.E., Lancaster, K.M.

(2024) J Inorg Biochem 260: 112682-112682

PubMed: 39094246 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jinorgbio.2024.112682
Primary Citation Related Structures:
9CQ5

PubMed Abstract:
The rate of photosynthesis and, thus, CO ₂ fixation, is limited by the rate of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Not only does Rubisco have a relatively low catalytic rate, but it also is promiscuous regarding the metal identity in the active site of the large subunit. In Nature, Rubisco binds either Mg(II) or Mn(II), depending on the chloroplastic ratio of these metal ions; most studies performed with Rubisco have focused on Mg-bound Rubisco. Herein, we report the first crystal structure of a Mn-bound Rubisco, and we compare its structural properties to those of its Mg-bound analogues.

Organizational Affiliation

Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA.

Macromolecule Content

Total Structure Weight: 543.2 kDa
Atom Count: 38,560
Modeled Residue Count: 4,720
Deposited Residue Count: 4,784
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, C, D, E A, B, C, D, E, F, G, H	475	Spinacia oleracea	Mutation(s): 0 EC: 4.1.1.39
UniProt
Find proteins for P00875 (Spinacia oleracea) Explore P00875 Go to UniProtKB: P00875
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00875
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 subunit, chloroplastic 2	I, J, K, L, M I, J, K, L, M, N, O, P	123	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for Q43832 (Spinacia oleracea) Explore Q43832 Go to UniProtKB: Q43832
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q43832
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAP (Subject of Investigation/LOI) Query on CAP Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain X [auth D] SDF format, chain V [auth C] SDF format, chain T [auth B] SDF format, chain R [auth A] SDF format, chain FA [auth H] SDF format, chain DA [auth G] SDF format, chain BA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain X [auth D] MOL2 format, chain V [auth C] MOL2 format, chain T [auth B] MOL2 format, chain R [auth A] MOL2 format, chain FA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain BA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain X [auth D] mmCIF format, chain V [auth C] mmCIF format, chain T [auth B] mmCIF format, chain R [auth A] mmCIF format, chain FA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain BA [auth F]	BA [auth F] DA [auth G] FA [auth H] R [auth A] T [auth B] BA [auth F], DA [auth G], FA [auth H], R [auth A], T [auth B], V [auth C], X [auth D], Z [auth E]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C₆ H₁₄ O₁₃ P₂ ITHCSGCUQDMYAI-ZMIZWQJLSA-N		Interactions Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain W [auth D] SDF format, chain U [auth C] SDF format, chain S [auth B] SDF format, chain Q [auth A] SDF format, chain EA [auth H] SDF format, chain CA [auth G] SDF format, chain AA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain W [auth D] MOL2 format, chain U [auth C] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain EA [auth H] MOL2 format, chain CA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain W [auth D] mmCIF format, chain U [auth C] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain EA [auth H] mmCIF format, chain CA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] CA [auth G] EA [auth H] Q [auth A] S [auth B] AA [auth F], CA [auth G], EA [auth H], Q [auth A], S [auth B], U [auth C], W [auth D], Y [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth E]