3f56

The structure of a previously undetected carboxysome shell protein: CsoS1D from Prochlorococcus marinus MED4

Method: X-RAY DIFFRACTION

▼

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

CsoS1D

Prochlorococcus marinus subsp. pastoris str. CCMP1986

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7V2D3_PROMP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 26–281； UniProt 1–256 Author chain B； PDBConstruct 26–281； UniProt 1–256 Author chain C； PDBConstruct 26–281； UniProt 1–256 Author chain D； PDBConstruct 26–281； UniProt 1–256 Author chain E； PDBConstruct 26–281； UniProt 1–256 Author chain F； PDBConstruct 26–281； UniProt 1–256

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3f56
Deposition date deposition_date	2008-11-03
Structure title title	The structure of a previously undetected carboxysome shell protein: CsoS1D from Prochlorococcus marinus MED4
Keywords keywords	Carboxysome, Hexamer, Structural Protein; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3f56__assembly_1__model_1

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

Download this curve (.dat)

3f56__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f56__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.92 Å
Rg (electron density)	29.78 Å
Total Rg	30.37 Å
Atom count	9269
Residues	1190
Excluded volume	166180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f56__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

▼

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3f56A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1710 — BMC (bacterial microcompartment) domain

Domain ID domain_id	3f56A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1710 — BMC (bacterial microcompartment) domain

Domain ID domain_id	3f56B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1710 — BMC (bacterial microcompartment) domain

Domain ID domain_id	3f56B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1710 — BMC (bacterial microcompartment) domain

Domain ID domain_id	3f56C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1710 — BMC (bacterial microcompartment) domain

Domain ID domain_id	3f56C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1710 — BMC (bacterial microcompartment) domain

Domain ID domain_id	3f56D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1710 — BMC (bacterial microcompartment) domain

Domain ID domain_id	3f56D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1710 — BMC (bacterial microcompartment) domain

Domain ID domain_id	3f56E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1710 — BMC (bacterial microcompartment) domain

Domain ID domain_id	3f56E02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1710 — BMC (bacterial microcompartment) domain

Domain ID domain_id	3f56F01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1710 — BMC (bacterial microcompartment) domain

Domain ID domain_id	3f56F02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1710 — BMC (bacterial microcompartment) domain

▶

Unit-cell length a length_a	122.410 Å
Unit-cell length b length_b	131.286 Å
Unit-cell length c length_c	131.762 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.303 Å
Low-resolution limit resolution_low	46.501 Å
R factor r_factor	0.1895
R_work r_work	0.1880
R_free r_free	0.2167

Description description	CsoS1D
Molecular weight formula_weight	31001.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	9951

The structure of a previously undetected carboxysome shell protein: CsoS1D from Prochlorococcus marinus MED4

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

CsoS1D

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

3f56__assembly_1__model_1

3f56__assembly_1__model_1 | I(q)

3f56__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Source organism organism	Prochlorococcus marinus subsp. pastoris str. CCMP1986
NCBI taxonomy ID ncbi_taxonomy_id	59919
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	682

The structure of a previously undetected carboxysome shell protein: CsoS1D from Prochlorococcus marinus MED4

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

CsoS1D

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

3f56__assembly_1__model_1

3f56__assembly_1__model_1 | I(q)

3f56__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)