3dn9

Carboxysome Subunit, CcmK1 C-terminal deletion mutant

Method: X-RAY DIFFRACTION

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

CcmK1 C-terminal deletion mutant

Synechocystis sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	SULFATE ION × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCMK1_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–91； UniProt 1–91 Author chain B； PDBConstruct 1–91； UniProt 1–91 Author chain C； PDBConstruct 1–91； UniProt 1–91 Author chain D； PDBConstruct 1–91； UniProt 1–91 Author chain E； PDBConstruct 1–91； UniProt 1–91 Author chain F； PDBConstruct 1–91； UniProt 1–91

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	3dn9
Deposition date deposition_date	2008-07-01
Structure title title	Carboxysome Subunit, CcmK1 C-terminal deletion mutant
Keywords keywords	hexamer, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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.

3dn9__assembly_1__model_1

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

Download this curve (.dat)

3dn9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dn9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.79 Å
Rg (electron density)	25.28 Å
Total Rg	26.25 Å
Atom count	3986
Residues	534
Excluded volume	71423 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dn9__assembly_1__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	CcmK1 C-terminal deletion mutant
Molecular weight formula_weight	10724.3 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	4066

MSIAVGMIETLGFPAVVEAADSMVKAARVTLVGYEKIGSGRVTVIVRGDVSEVQASVTAGIENIRRVNGGEVLSNHIIARPHENLEYVLPILEHHHHHH

Source Source

Source organism organism	Synechocystis sp.
NCBI taxonomy ID ncbi_taxonomy_id	1148
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	58

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d3dn9a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.56 — CcmK-like
Family Family family	d.58.56.1 — CcmK-like

Domain ID domain_id	d3dn9b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.56 — CcmK-like
Family Family family	d.58.56.1 — CcmK-like

Domain ID domain_id	d3dn9b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3dn9c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.56 — CcmK-like
Family Family family	d.58.56.1 — CcmK-like

Domain ID domain_id	d3dn9d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.56 — CcmK-like
Family Family family	d.58.56.1 — CcmK-like

Domain ID domain_id	d3dn9d2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3dn9e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.56 — CcmK-like
Family Family family	d.58.56.1 — CcmK-like

Domain ID domain_id	d3dn9f1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.56 — CcmK-like
Family Family family	d.58.56.1 — CcmK-like

Domain ID domain_id	d3dn9f2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	3dn9A00
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	3dn9B00
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	3dn9C00
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	3dn9D00
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	3dn9E00
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	3dn9F00
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

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Unit-cell length a length_a	49.204 Å
Unit-cell length b length_b	49.194 Å
Unit-cell length c length_c	49.211 Å
Unit-cell angle α angle_alpha	90.65 °
Unit-cell angle β angle_beta	91.41 °
Unit-cell angle γ angle_gamma	91.43 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.280 Å
Low-resolution limit resolution_low	17.610 Å
R factor r_factor	0.2240
R_work r_work	0.2220
R_free r_free	0.2740

Carboxysome Subunit, CcmK1 C-terminal deletion mutant

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

CcmK1 C-terminal deletion mutant

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

3dn9__assembly_1__model_1

3dn9__assembly_1__model_1 | I(q)

3dn9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Carboxysome Subunit, CcmK1 C-terminal deletion mutant

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

CcmK1 C-terminal deletion mutant

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

3dn9__assembly_1__model_1

3dn9__assembly_1__model_1 | I(q)

3dn9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)