SAXSdb — 7d6c

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

Carbon dioxide concentrating mechanism protein CcmM

Synechococcus elongatus (strain PCC 7942 / FACHB-805)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Carboxysome assembly protein CcmN × 2 （P46204） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Carboxysome assembly protein CcmN × 2 （P46204） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCMM_SYNE7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 10–218； UniProt 1–209 Author chain 2； PDBConstruct 10–218； UniProt 1–209

Carboxysome assembly protein CcmN

Synechococcus elongatus (strain PCC 7942 / FACHB-805)

UniProt P46204

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Carbon dioxide concentrating mechanism protein CcmM × 1 （Q03513） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Carbon dioxide concentrating mechanism protein CcmM × 1 （Q03513） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCMN_SYNE7
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain 3； PDBConstruct 5–122； UniProt 1–118 Author chain 4； PDBConstruct 5–122； UniProt 1–118 Author chain 5； PDBConstruct 5–122； UniProt 1–118 Author chain F； PDBConstruct 5–122； UniProt 1–118

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	7d6c
Deposition date deposition_date	2020-09-30
Structure title title	Crystal structure of CcmM N-terminal domain in complex with CcmN
Keywords keywords	CO2-concentrating mechanism, carboxysome, scaffolding protein, complex, 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.

7d6c__assembly_1__model_1

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

Download this curve (.dat)

7d6c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7d6c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.28 Å
Rg (electron density)	21.04 Å
Total Rg	21.85 Å
Atom count	2802
Residues	392
Excluded volume	50074 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7d6c__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7d6c__assembly_2__model_1`	trimeric （3）	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	Carbon dioxide concentrating mechanism protein CcmM
Molecular weight formula_weight	23250.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2
Atom count atom_count	5696

MDYKDDDDKMPSPTTVPVATAGRLAEPYIDPAAQVHAIASIIGDVRIAAGVRVAAGVSIRADEGAPFQVGKESILQEGAVIHGLEYGRVLGDDQADYSVWIGQRVAITHKALIHGPAYLGDDCFVGFRSTVFNARVGAGSVIMMHALVQDVEIPPGRYVPSGAIITTQQQADRLPEVRPEDREFARHIIGSPPVIVRSTPAATADFHSTPTPSPLRPS

Source Source

Source organism organism	Synechococcus elongatus (strain PCC 7942 / FACHB-805)
NCBI taxonomy ID ncbi_taxonomy_id	1140
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Carboxysome assembly protein CcmN
Molecular weight formula_weight	12087.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3,4,5,F

FQSNMHLPPLEPPISDRYFASGEVTIAADVVIAPGVLLIAEADSRIEIASGVCIGLGSVIHARGGAIIIQAGALLAAGVLIVGQSIVGRQACLGASTTLVNTSIEAGGVTAPGSLLSAETPP

Source Source

Source organism organism	Synechococcus elongatus (strain PCC 7942 / FACHB-805)
NCBI taxonomy ID ncbi_taxonomy_id	1140
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	7d6c401
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	7d6c501
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	7d6cF01
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

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Unit-cell length a length_a	84.180 Å
Unit-cell length b length_b	92.330 Å
Unit-cell length c length_c	125.380 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.890 Å
Low-resolution limit resolution_low	44.160 Å
R factor r_factor	0.2117
R_work r_work	0.2086
R_free r_free	0.2720

Crystal structure of CcmM N-terminal domain in complex with CcmN

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

Carbon dioxide concentrating mechanism protein CcmM

State in the Current Structure

Other States of the Same Protein in the Database

Carboxysome assembly protein CcmN

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

7d6c__assembly_1__model_1

7d6c__assembly_1__model_1 | I(q)

7d6c__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of CcmM N-terminal domain in complex with CcmN

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

Carbon dioxide concentrating mechanism protein CcmM

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Carboxysome assembly protein CcmN

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

7d6c__assembly_1__model_1

7d6c__assembly_1__model_1 | I(q)

7d6c__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)