SAXSdb — 9i26

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

Ribulose bisphosphate carboxylase

Rhodospirillum rubrum ATCC 11170

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–466 Chain B； UniProt 1–466	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；Inactive CbbM in 20 mM Tris buffer (pH 8.5), containing 100 mM NaCl was mixed with condition comprised of 1.2 M ammonium chloride, 100 mM MES (pH 6), 20 %(w/v) PEG6000 in a 1:1 ratio with a final drop volume of 1 micro liter. The mother liquor was supplemented with 30% (v/v) PEG200, before the crystals were plunge frozen in liquid nitrogen	Resolution 2.30 Å R-free 0.226

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 9I26	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7VWX CryoEM structure of football-shaped GroEL:ES2 with RuBisCO Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 29 PDB declaration: 29-meric	Chain a 1–466（466 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.60 Å
8BAA CryoEM structure of GroEL-GroES-ADP.AlF3-Rubisco, class II. Deposited 2022-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric	Chain Z 1–466（466 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 7 MG MAGNESIUM ION × 14 ADP ADENOSINE-5'-DIPHOSPHATE × 14 K POTASSIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；The grid was prepared using a chameleon (SPT Labtech).	Resolution 4.20 Å
9I27 activated Form II Rubisco from Rhodospirillum rubrum with bound Magnesium and CABP Deposited 2025-01-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–466（466 aa） Chain B 1–466（466 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；289 K；Crystallization of activated CbbM in buffer containing 20 mM Tris (pH 8.5), 100 mM NaCl, 0.2 mM CABP, and 10 mM sodium bicarbonate was mixed with a condition containing 200 mM Bis-Tris propane (pH 7.3) and 20 % (w/v) PEG4000. Prior to plung freezing the crystals in liquid nitrogen the mother liquor was supplemented with 33 % (v/v) PEG200.	Resolution 2.30 Å R-free 0.217
9I28 Form II Rubisco inside EPYC1-formed liquid-liquid phase separated condensates with bound Magnesium and CABP Deposited 2025-01-20	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–466（466 aa） Chain B 1–466（466 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE；sample was blotted for 3 s with blot force 20	Resolution 2.93 Å

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

View Construct and Data Evidence

UniProt name	RBL2_RHORT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–466； UniProt 1–466 Author chain B； PDBConstruct 1–466； UniProt 1–466

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	9i26
Deposition date deposition_date	2025-01-20
最后修订 last_revision	2026-02-04
Structure title title	inactive Form II Rubisco from Rhodospirillum rubrum
Keywords keywords	ribulose-1, 5-bisphosphate carboxylase/oxygenase, Rubisco, 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	29.95 Å
Radius of gyration Rg (electron density) rg_electron	29.05 Å
Forward intensity I(0) i0	129397000.00
Molecular weight molecular_weight	90253.0 kDa
Excluded volume excluded_volume	112840 Å³
Envelope volume envelope_volume	135860 Å³
Hydration-shell volume shell_volume	38703 Å³
Envelope diameter envelope_diameter	109.0 Å
Shell Rg shell_rg	36.53 Å
Envelope Rg envelope_rg	29.14 Å
Shape Rg shape_rg	29.08 Å
Total Rg total_rg	29.61 Å
Total atoms total_atoms	6369
Residues n_residues	830
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	103.2 Å
Rg (real space) rg_real	29.93 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	1.2940e+08
I(0) uncertainty (real space) i0_real_error	1.9900e+06
Rg (reciprocal space) rg_reciprocal	29.94 Å
I(0) (reciprocal space) i0_reciprocal	129400000.0000
Solution quality estimate total_estimate	0.8670
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.0 Å
Skewness Skewness skewness	0.385
Kurtosis Kurtosis kurtosis	-0.080
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31640000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.769; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.968

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Ribulose bisphosphate carboxylase
Molecular weight formula_weight	50538.9 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6524

MDQSSRYVNLALKEEDLIAGGEHVLCAYIMKPKAGYGYVATAAHFAAESSTGTNVEVCTTDDFTRGVDALVYEVDEARELTKIAYPVALFDRNITDGKAMIASFLTLTMGNNQGMGDVEYAKMHDFYVPEAYRALFDGPSVNISALWKVLGRPEVDGGLVVGTIIKPKLGLRPKPFAEACHAFWLGGDFIKNDEPQGNQPFAPLRDTIALVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYVLETFGENASHVALLVDGYVAGAAAITTARRRFPDNFLHYHRAGHGAVTSPQSKRGYTAFVHCKMARLQGASGIHTGTMGFGKMEGESSDRAIAYMLTQDEAQGPFYRQSWGGMKACTPIISGGMNALRMPGFFENLGNANVILTAGGGAFGHIDGPVAGARSLRQAWQAWRDGVPVLDYAREHKELARAFESFPGDADQIYPGWRKALGVEDTRSALPA

来源 Source

来源生物 organism	Rhodospirillum rubrum ATCC 11170
NCBI Class编号 ncbi_taxonomy_id	269796
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	155

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8. Citations (1)

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Unit-cell length a length_a	78.980 Å
Unit-cell length b length_b	78.980 Å
Unit-cell length c length_c	277.230 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	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	29.450 Å
R factor r_factor	0.2048
R_work r_work	0.2036
R_free r_free	0.2263

fit	/app/data/saxs_computation/i2/9i26/9i26.fit
pddf	/app/data/pr_computation/i2/9i26/9i26.pr.out
profile	/app/data/saxs_computation/i2/9i26/9i26.dat

inactive Form II Rubisco from Rhodospirillum rubrum

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

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)