SAXSdb — 25hn

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

Ribulose bisphosphate carboxylase large chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Ribulose bisphosphate carboxylase small subunit × 8 （Q2YB79） ZINC ION × 8 water × 16	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBL_NITMU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–489； UniProt 1–489 Author chain C； PDBConstruct 1–489； UniProt 1–489 Author chain E； PDBConstruct 1–489； UniProt 1–489 Author chain F； PDBConstruct 1–489； UniProt 1–489 Author chain I； PDBConstruct 1–489； UniProt 1–489 Author chain J； PDBConstruct 1–489； UniProt 1–489 Author chain M； PDBConstruct 1–489； UniProt 1–489 Author chain N； PDBConstruct 1–489； UniProt 1–489

Ribulose bisphosphate carboxylase small subunit

OrganismNot specified

UniProt Q2YB79

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Ribulose bisphosphate carboxylase large chain × 8 （Q2YB78） ZINC ION × 8 water × 16	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2YB79_NITMU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–144； UniProt 1–144 Author chain D； PDBConstruct 1–144； UniProt 1–144 Author chain G； PDBConstruct 1–144； UniProt 1–144 Author chain H； PDBConstruct 1–144； UniProt 1–144 Author chain K； PDBConstruct 1–144； UniProt 1–144 Author chain L； PDBConstruct 1–144； UniProt 1–144 Author chain O； PDBConstruct 1–144； UniProt 1–144 Author chain P； PDBConstruct 1–144； UniProt 1–144

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	25hn
Deposition date deposition_date	2026-04-03
Structure title title	Cryo-EM structure of native Rubisco from Nitrosospira multiformis
Keywords keywords	rubisco, carbon fixation, nitrifying bacterium, autotrophy, cryo-EM, LYASE; LYASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

25hn__assembly_1__model_1

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

Download this curve (.dat)

25hn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

25hn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.68 Å
Rg (electron density)	46.95 Å
Total Rg	47.25 Å
Atom count	37888
Residues	4784
Excluded volume	673430 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`25hn__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 (4)

Entity 1 Entity 1 polymer

Description description	Ribulose bisphosphate carboxylase large chain
Molecular weight formula_weight	54379.9 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,F,I,J,M,N
Atom count atom_count	38393

MSEAITGAERYKSGVIPYKKMGYWEPDYVPKDTDIIAMFRITPQAGVEPEEAAAAVAGESSTATWTVVWTDRLTACELYRAKAFRTDPVPNTGEGTKTEQQYFAYIAYDLDLFEPGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGIIVERERLDKFGRPLLGATTKPKLGLSGRNYGRVVYEGLKGGLDFMKDDENINSQPFMHWRDRFLYCMEAVNKASAATGEVKGHYLNVTAGTMEEMYERAEFAKSLGSVIIMIDLVIGYTAIQSMAKWARKNDMILHLHRAGNSTYSRQKNHGMNFRVICKWMRMAGVDHIHAGTVVGKLEGDPLMIKGFYDTLRDRHTPVSLEHGLFFEQDWASLNKVMPVASGGIHAGQMHQLLDYLGEDVILQFGGGTIGHPQGIQAGAVANRVALEAMIMARNEGRDYVKEGPQILEEAAKWCTPLKLALDTWKDITFNYESTDTADFVPSETASV

Entity 2 Entity 2 polymer

Description description	Ribulose bisphosphate carboxylase small subunit
Molecular weight formula_weight	16805.9 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,G,H,K,L,O,P

MMTNFQNRLTQGQFSFLPPLTDKQISAQIKYALKNNWAIGIEYTDDPHPRNTYWEMFGNPMFDLKDPAGILQEINDCRKTYPNHYIRVTAFDSSRGVESPAMSYIVNRPKNEPGFGLVRQEVDGRQIRYTVHSYATEKPEAERY

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	433

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.260 Å
Low-resolution limit resolution_low	138.787 Å
R factor r_factor	—
R_work r_work	0.2850
R_free r_free	—

Resolution resolution	2.26 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	64288

Cryo-EM structure of native Rubisco from Nitrosospira multiformis

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

Ribulose bisphosphate carboxylase large chain

State in the Current Structure

Other States of the Same Protein in the Database

Ribulose bisphosphate carboxylase small subunit

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

25hn__assembly_1__model_1

25hn__assembly_1__model_1 | I(q)

25hn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Cryo-EM structure of native Rubisco from Nitrosospira multiformis

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

Ribulose bisphosphate carboxylase large 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

Ribulose bisphosphate carboxylase small 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

25hn__assembly_1__model_1

25hn__assembly_1__model_1 | I(q)

25hn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)