4lf2

Hexameric Form II RuBisCO from Rhodopseudomonas palustris, activated and complexed with sulfate and magnesium

Method: X-RAY DIFFRACTION

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

Ribulose bisphosphate carboxylase

Rhodopseudomonas palustris

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	MAGNESIUM ION × 4 SULFATE ION × 12 CARBONATE ION × 3 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 SULFATE ION × 4 CARBONATE ION × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 SULFATE ION × 4 CARBONATE ION × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBL2_RHOPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–481； UniProt 1–461 Author chain B； PDBConstruct 21–481； UniProt 1–461 Author chain C； PDBConstruct 21–481； UniProt 1–461 Author chain D； PDBConstruct 21–481； UniProt 1–461 Author chain E； PDBConstruct 21–481； UniProt 1–461 Author chain F； PDBConstruct 21–481； UniProt 1–461

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	4lf2
Deposition date deposition_date	2013-06-26
Structure title title	Hexameric Form II RuBisCO from Rhodopseudomonas palustris, activated and complexed with sulfate and magnesium
Keywords keywords	;Form II, CbbM 2-CABP, Transition-State Analog, Reaction Intermediate Analogue, photosynthesis, photosynthetic carbon fixation, lyase, oxidoreductase ;; lyase, oxidoreductase
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.

4lf2__assembly_1__model_1

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

Download this curve (.dat)

4lf2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4lf2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.07 Å
Rg (electron density)	40.20 Å
Total Rg	40.59 Å
Atom count	21205
Residues	2725
Excluded volume	374120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4lf2__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4lf2__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4lf2__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4lf2__assembly_4__model_1`	dimeric （2）	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 bisphosphate carboxylase
Molecular weight formula_weight	52757.3 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	22617

MGSSHHHHHHSSGLVPRGSHMDQSNRYANLNLKESELIAGGRHVLCAYIMKPKAGFGNFIQTAAHFAAESSTGTNVEVSTTDDFTRGVDALVYEVDEANSLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFADNADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKLKPQAA

Source Source

Source organism organism	Rhodopseudomonas palustris
NCBI taxonomy ID ncbi_taxonomy_id	258594
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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	12

Entity 4 Entity 4 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1362

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d4lf2a1
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.58.9.0 — automated matches

Domain ID domain_id	d4lf2a2
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	d4lf2b1
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.58.9.0 — automated matches

Domain ID domain_id	d4lf2b2
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	d4lf2c1
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.58.9.0 — automated matches

Domain ID domain_id	d4lf2c2
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	d4lf2d1
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.58.9.0 — automated matches

Domain ID domain_id	d4lf2d2
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	d4lf2e1
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.58.9.0 — automated matches

Domain ID domain_id	d4lf2e2
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	d4lf2f1
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.58.9.0 — automated matches

Domain ID domain_id	d4lf2f2
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

CATH v4.4 (12 domains)

Domain ID domain_id	4lf2A01
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	4lf2A02
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	4lf2B01
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	4lf2B02
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	4lf2C01
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	4lf2C02
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	4lf2D01
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	4lf2D02
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	4lf2E01
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	4lf2E02
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	4lf2F01
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	4lf2F02
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

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Unit-cell length a length_a	74.221 Å
Unit-cell length b length_b	99.777 Å
Unit-cell length c length_c	100.000 Å
Unit-cell angle α angle_alpha	67.30 °
Unit-cell angle β angle_beta	71.28 °
Unit-cell angle γ angle_gamma	86.63 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.380 Å
Low-resolution limit resolution_low	87.430 Å
R factor r_factor	0.2053
R_work r_work	0.2026
R_free r_free	0.2576

Hexameric Form II RuBisCO from Rhodopseudomonas palustris, activated and complexed with sulfate and magnesium

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

Ribulose bisphosphate carboxylase

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

4lf2__assembly_1__model_1

4lf2__assembly_1__model_1 | I(q)

4lf2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Hexameric Form II RuBisCO from Rhodopseudomonas palustris, activated and complexed with sulfate and magnesium

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

Ribulose bisphosphate carboxylase

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

4lf2__assembly_1__model_1

4lf2__assembly_1__model_1 | I(q)

4lf2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)