SAXSdb — 3rub

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1. Protein Identity and Related Structures Protein Identity & Related Structures

RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III

Nicotiana tabacum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III × 8 （P69249） SULFATE ION × 24 ASPARAGINE × 8 water × 16	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBL_TOBAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain L； PDBConstruct 1–477； UniProt 1–477

RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III

OrganismNot specified

UniProt P69249

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III × 8 （P00876） SULFATE ION × 24 ASPARAGINE × 8 water × 16	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBS_TOBAC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain S； PDBConstruct 1–123； UniProt 58–180

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3rub
Deposition date deposition_date	1990-05-25
Structure title title	CRYSTAL STRUCTURE OF THE UNACTIVATED FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM TOBACCO REFINED AT 2.0-ANGSTROMS RESOLUTION
Keywords keywords	LYASE(CARBON-CARBON); LYASE(CARBON-CARBON)
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3rub__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3rub__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3rub__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	46.73 Å
Rg (electron density)	46.05 Å
Total Rg	46.43 Å
Atom count	36000
Residues	4512
Excluded volume	638640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3rub__assembly_1__model_1`	hexadecameric （16）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III
Molecular weight formula_weight	53041.2 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	4716

MSPQTETKASVGFKAGVKEYKLTYYTPEYQTKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIERVVGEKDQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFVEQDRSRGIYFTQDWVSLPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGMTLGHPWGNAPGAVANRVALEACVKARNEGRDLAQEGNEIIREACKWSPELAAACEVWKEIVFNFAAVDVLDK

Source Source

Source organism organism	Nicotiana tabacum
Common name common_name	tobacco
NCBI taxonomy ID ncbi_taxonomy_id	4097

Entity 2 Entity 2 polymer

Description description	RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III
Molecular weight formula_weight	14573.6 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

MQVWPPINKKKYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFETEHGFVYRENNKSPGYYDGRYWTMWKLPMFGCTDATQVLAEVEEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKPEGY

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	ASPARAGINE
Molecular weight formula_weight	132.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	216

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3rubl1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d3rubl2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

Domain ID domain_id	d3rubs_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

CATH v4.4 (3 domains)

Domain ID domain_id	3rubL01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

Domain ID domain_id	3rubL02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

Domain ID domain_id	3rubS00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

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Unit-cell length a length_a	148.700 Å
Unit-cell length b length_b	148.700 Å
Unit-cell length c length_c	137.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1710
R_work r_work	—
R_free r_free	—

CRYSTAL STRUCTURE OF THE UNACTIVATED FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM TOBACCO REFINED AT 2.0-ANGSTROMS RESOLUTION

1. Protein Identity and Related Structures Protein Identity & Related Structures

RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III

State in the Current Structure

Other States of the Same Protein in the Database

RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3rub__assembly_1__model_1

3rub__assembly_1__model_1 | I(q)

3rub__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (4)

CRYSTAL STRUCTURE OF THE UNACTIVATED FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM TOBACCO REFINED AT 2.0-ANGSTROMS RESOLUTION

1. Protein Identity and Related Structures Protein Identity & Related Structures

RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3rub__assembly_1__model_1

3rub__assembly_1__model_1 | I(q)

3rub__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (4)