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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–473	Not recorded	Ribulose bisphosphate carboxylase small chain × 1 （P45686） SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；ammonium sulfate, citrate, cobalt chloride, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.166
2	Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain A； UniProt 1–473	Not recorded	Ribulose bisphosphate carboxylase small chain × 8 （P45686） SO4 SULFATE ION × 16 GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；ammonium sulfate, citrate, cobalt chloride, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.166
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–473	Not recorded	Ribulose bisphosphate carboxylase small chain × 2 （P45686） SO4 SULFATE ION × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；ammonium sulfate, citrate, cobalt chloride, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.166
4	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–473	Not recorded	Ribulose bisphosphate carboxylase small chain × 2 （P45686） SO4 SULFATE ION × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；ammonium sulfate, citrate, cobalt chloride, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.166

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1SVD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6UEW Rubisco / CsoS2 N-peptide complex responsible for alpha-carboxysome cargo loading Deposited 2019-09-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 2–473（472 aa） Chain C 2–473（472 aa） Chain E 2–473（472 aa） Chain G 2–473（472 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 400, magnesium chloride, HEPES	Resolution 2.40 Å R-free 0.259
7SMK H. neapolitanus carboxysomal rubisco/CsoSCA-peptide (1-50)complex Deposited 2021-10-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 2–473（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3 seconds	Resolution 1.98 Å
7SNV H. neapolitanus carboxysomal rubisco/CsoSCA-peptide (1-50)complex Deposited 2021-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 2–473（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3 seconds	Resolution 2.07 Å
7ZBT Subtomogram averaging of Rubisco from native Halothiobacillus carboxysomes Deposited 2022-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–473（473 aa） Chain B 1–473（473 aa） Chain C 1–473（473 aa） Chain D 1–473（473 aa） Chain E 1–473（473 aa） Chain F 1–473（473 aa） Chain G 1–473（473 aa） Chain H 1–473（473 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain M； UniProt 1–110	Not recorded	ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit × 1 （O85040） SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；ammonium sulfate, citrate, cobalt chloride, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.166
2	Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain M； UniProt 1–110	Not recorded	ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit × 8 （O85040） SO4 SULFATE ION × 16 GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；ammonium sulfate, citrate, cobalt chloride, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.166
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain M； UniProt 1–110	Not recorded	ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit × 2 （O85040） SO4 SULFATE ION × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；ammonium sulfate, citrate, cobalt chloride, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.166
4	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain M； UniProt 1–110	Not recorded	ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit × 2 （O85040） SO4 SULFATE ION × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；ammonium sulfate, citrate, cobalt chloride, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.166

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1SVD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6UEW Rubisco / CsoS2 N-peptide complex responsible for alpha-carboxysome cargo loading Deposited 2019-09-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain B 1–110（110 aa） Chain D 1–110（110 aa） Chain F 1–110（110 aa） Chain H 1–110（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 400, magnesium chloride, HEPES	Resolution 2.40 Å R-free 0.259
7SMK H. neapolitanus carboxysomal rubisco/CsoSCA-peptide (1-50)complex Deposited 2021-10-26	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain B 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3 seconds	Resolution 1.98 Å
7SNV H. neapolitanus carboxysomal rubisco/CsoSCA-peptide (1-50)complex Deposited 2021-10-28	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain B 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3 seconds	Resolution 2.07 Å
7ZBT Subtomogram averaging of Rubisco from native Halothiobacillus carboxysomes Deposited 2022-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa） Chain O 1–110（110 aa） Chain P 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.41 Å
Radius of gyration Rg (electron density) rg_electron	25.89 Å
Forward intensity I(0) i0	63761300.00
Molecular weight molecular_weight	62165.0 kDa
Excluded volume excluded_volume	77604 Å³
Envelope volume envelope_volume	93040 Å³
Hydration-shell volume shell_volume	30146 Å³
Envelope diameter envelope_diameter	91.7 Å
Shell Rg shell_rg	33.07 Å
Envelope Rg envelope_rg	26.42 Å
Shape Rg shape_rg	25.90 Å
Total Rg total_rg	26.60 Å
Total atoms total_atoms	4385
Residues n_residues	553
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	87.2 Å
Rg (real space) rg_real	26.45 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	6.3760e+07
I(0) uncertainty (real space) i0_real_error	8.4570e+05
Rg (reciprocal space) rg_reciprocal	26.44 Å
I(0) (reciprocal space) i0_reciprocal	63760000.0000
Solution quality estimate total_estimate	0.8855
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.1 Å
Skewness Skewness skewness	0.410
Kurtosis Kurtosis kurtosis	-0.270
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21840000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.955

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/sv/1svd/1svd.fit
pddf	/app/data/pr_computation/sv/1svd/1svd.pr.out
profile	/app/data/saxs_computation/sv/1svd/1svd.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. 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

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)