4RUB | pdb_00004rub

A CRYSTAL FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM NICOTIANA TABACUM IN THE ACTIVATED STATE

PDB DOI: https://doi.org/10.2210/pdb4RUB/pdb

Classification: LYASE(CARBON-CARBON)
Organism(s): Nicotiana tabacum
Mutation(s): No

Deposited: 1990-05-25 Released: 1992-10-15
Deposition Author(s): Schreuder, H., Cascio, D., Curmi, P.M.G., Eisenberg, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

A crystal form of ribulose-1,5-bisphosphate carboxylase/oxygenase from Nicotiana tabacum in the activated state.

Suh, S.W., Cascio, D., Chapman, M.S., Eisenberg, D.

(1987) J Mol Biology 197: 363-365

PubMed: 3681999 Search on PubMed
DOI: https://doi.org/10.1016/0022-2836(87)90129-x
Primary Citation Related Structures:
4RUB

PubMed Abstract:
A new crystal form of ribulose-1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39) from Nicotiana tabacum has been obtained at alkaline pH with polyethylene glycol 8000 in the presence of a non-ionic detergent, beta-octyl glucoside. The crystals are grown at room temperature by the hanging-drop vapor diffusion technique from a protein solution containing enzyme complexed with CO2, Mg2+, and the transition state analog 2-C-carboxy-D-arabinitol-1,5-bisphosphate. The crystals belong to the the space group P3(1)21 (or P3(2)21) with the cell parameters a = 204.6 A, and c = 117.4 A (1 A = 0.1 nm). The asymmetric unit contains half (L4S4: L, large subunit, 53,000 Mr; S, small subunit, 15,000 Mr) of a hexadecameric molecule (L8S8, 540,000 Mr). The crystals diffract to at least 2.6 A Bragg spacing and are suitable for X-ray structure determination.

Organizational Affiliation

Molecular Biology Institute, University of California, Los Angeles 90024.

Macromolecule Content

Total Structure Weight: 271.58 kDa
Atom Count: 18,708
Modeled Residue Count: 2,352
Deposited Residue Count: 2,400
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)	A, C [auth B], E [auth C], G [auth D]	477	Nicotiana tabacum	Mutation(s): 0 EC: 4.1.1.39
UniProt
Find proteins for P00876 (Nicotiana tabacum) Explore P00876 Go to UniProtKB: P00876
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00876
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)	B [auth S], D [auth T], F [auth U], H [auth V]	123	Nicotiana tabacum	Mutation(s): 0 EC: 4.1.1.39
UniProt
Find proteins for P69249 (Nicotiana tabacum) Explore P69249 Go to UniProtKB: P69249
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69249
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 S [auth D] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain J [auth A] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A]	J [auth A], M [auth B], P [auth C], S [auth D]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C₆ H₁₄ O₁₃ P₂ ITHCSGCUQDMYAI-ZMIZWQJLSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain K [auth A] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A]	K [auth A], N [auth B], Q [auth C], T [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A], L [auth B], O [auth C], R [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Observed: 0.202 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.6	α = 90
b = 204.6	β = 90
c = 117.4	γ = 120

Software Package:

Software Name	Purpose
PROFFT	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 1992-10-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1992-10-15
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-06-05
Changes: Data collection, Database references, Derived calculations, Other