SAXSdb — 1svd

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

ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ribulose bisphosphate carboxylase small chain × 1 （P45686） SULFATE ION × 2 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 16	Ribulose bisphosphate carboxylase small chain × 8 （P45686） SULFATE ION × 16 GLYCEROL × 8 water × 16	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Ribulose bisphosphate carboxylase small chain × 2 （P45686） SULFATE ION × 4 GLYCEROL × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Ribulose bisphosphate carboxylase small chain × 2 （P45686） SULFATE ION × 4 GLYCEROL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O85040_THINE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–473； UniProt 1–473

Ribulose bisphosphate carboxylase small chain

OrganismNot specified

UniProt P45686

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit × 1 （O85040） SULFATE ION × 2 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 16	ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit × 8 （O85040） SULFATE ION × 16 GLYCEROL × 8 water × 16	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit × 2 （O85040） SULFATE ION × 4 GLYCEROL × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit × 2 （O85040） SULFATE ION × 4 GLYCEROL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBS_THINE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–110； UniProt 1–110

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	1svd
Deposition date deposition_date	2004-03-29
Structure title title	The structure of Halothiobacillus neapolitanus RuBisCo
Keywords keywords	beta-alpha-barrel, LYASE; LYASE
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.

1svd__assembly_1__model_1

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

Download this curve (.dat)

1svd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1svd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.41 Å
Rg (electron density)	25.89 Å
Total Rg	26.60 Å
Atom count	4385
Residues	553
Excluded volume	77604 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1svd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1svd__assembly_2__model_1`	hexadecameric （16）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1svd__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1svd__assembly_4__model_1`	tetrameric （4）	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 large subunit
Molecular weight formula_weight	52702.5 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4778

MAVKKYSAGVKEYRQTYWMPEYTPLDSDILACFKITPQPGVDREEAAAAVAAESSTGTWTTVWTDLLTDMDYYKGRAYRIEDVPGDDAAFYAFIAYPIDLFEEGSVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEIGAPIIMHDYITGGFTANTGLAKWCQDNGVLLHIHRAMHAVIDRNPNHGIHFRVLTKILRLSGGDHLHTGTVVGKLEGDRASTLGWIDLLRESFIPEDRSRGIFFDQDWGSMPGVFAVASGGIHVWHMPALVNIFGDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVEARNQGRDIEKEGKEILTAAAQHSPELKIAMETWKEIKFEFDTVDKLDTQNR

Entity 2 Entity 2 polymer

Description description	Ribulose bisphosphate carboxylase small chain
Molecular weight formula_weight	12866.6 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MAEMQDYKQSLKYETFSYLPPMNAERIRAQIKYAIAQGWSPGIEHVEVKNSMNQYWYMWKLPFFGEQNVDNVLAEIEACRSAYPTHQVKLVAYDNYAQSLGLAFVVYRGN

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	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	354

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1svda1
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	d1svda2
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	d1svdm1
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	1svdA01
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	1svdA02
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	1svdM00
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	157.066 Å
Unit-cell length b length_b	157.066 Å
Unit-cell length c length_c	107.609 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	1.800 Å
Low-resolution limit resolution_low	87.710 Å
R factor r_factor	0.1461
R_work r_work	0.1450
R_free r_free	0.1657

The structure of Halothiobacillus neapolitanus RuBisCo

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

ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit

State in the Current Structure

Other States of the Same Protein in the Database

Ribulose bisphosphate carboxylase small chain

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

1svd__assembly_1__model_1

1svd__assembly_1__model_1 | I(q)

1svd__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

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 (1)

The structure of Halothiobacillus neapolitanus RuBisCo

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

ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit

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 bisphosphate carboxylase small chain

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

1svd__assembly_1__model_1

1svd__assembly_1__model_1 | I(q)

1svd__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

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 (1)