SAXSdb — 6hba

▼

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

Carbon dioxide concentrating mechanism protein CcmM

Synechococcus elongatus (strain PCC 7942)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 225–313	Fragment：SSUL domain 1	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4.5；277 K；25.5% PEG-3350 and 0.1 M Na-acetate pH 4.5	Resolution 1.65 Å R-free 0.241
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 225–313	Fragment：SSUL domain 1	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4.5；277 K；25.5% PEG-3350 and 0.1 M Na-acetate pH 4.5	Resolution 1.65 Å R-free 0.241

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 6HBA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6HBB Crystal Structure of the small subunit-like domain 1 of CcmM from Synechococcus elongatus (strain PCC 7942) Deposited 2018-08-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 225–313（89 aa） Fragment：SSUL domain 1	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；277 K；1.95 M ammonium sulfate and 0.1 M Na-acetate pH 4.5	Resolution 1.20 Å R-free 0.195
6HBB Crystal Structure of the small subunit-like domain 1 of CcmM from Synechococcus elongatus (strain PCC 7942) Deposited 2018-08-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 225–313（89 aa） Fragment：SSUL domain 1	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；277 K；1.95 M ammonium sulfate and 0.1 M Na-acetate pH 4.5	Resolution 1.20 Å R-free 0.195
6HBC Structure of the repeat unit in the network formed by CcmM and Rubisco from Synechococcus elongatus Deposited 2018-08-10	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 225–313（89 aa） Fragment：SSUL domain 1	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Solutions were made fresh cryo-EM vitrification conditions Cryogen ETHANE；blot for 3 seconds before plunging	Resolution 2.78 Å
7D6C Crystal structure of CcmM N-terminal domain in complex with CcmN Deposited 2020-09-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain 1 1–209（209 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287.15 K；PEG 8000, N-(2-acetamido) iminodiacetic acid	Resolution 2.89 Å R-free 0.272
7D6C Crystal structure of CcmM N-terminal domain in complex with CcmN Deposited 2020-09-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain 2 1–209（209 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287.15 K；PEG 8000, N-(2-acetamido) iminodiacetic acid	Resolution 2.89 Å R-free 0.272
7O4Z Crystal structure of the carbonic anhydrase-like domain of CcmM from Synechococcus elongatus (strain PCC 7942) Deposited 2021-04-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–181（181 aa）	Not recorded	NI NICKEL (II) ION × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG-3350 and 0.1 M HEPES pH 7.5	Resolution 1.67 Å R-free 0.200
7O54 Crystal structure of the carbonic anhydrase-like domain of CcmM in complex with the C-terminal 17 residues of CcaA from Synechococcus elongatus (strain PCC 7942) Deposited 2021-04-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–181（181 aa）	Not recorded	NI NICKEL (II) ION × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG-3350 and 0.1 M HEPES pH 7.5	Resolution 1.63 Å R-free 0.200
9FWV Rubisco in native beta-carboxysomes Deposited 2024-07-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: 20-meric	Chain A 225–310（86 aa） Chain B 225–310（86 aa） Chain F 225–310（86 aa） Chain T 225–310（86 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CCMM_SYNE7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–92； UniProt 225–313 Author chain B； PDBConstruct 4–92； UniProt 225–313

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	6hba
Deposition date deposition_date	2018-08-10
Structure title title	Crystal Structure of the small subunit-like domain 1 of CcmM from Synechococcus elongatus (strain PCC 7942), thiol-oxidized form
Keywords keywords	alpha-beta structure, Rubisco, Carboxysome, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.13 Å
Radius of gyration Rg (electron density) rg_electron	18.21 Å
Forward intensity I(0) i0	8193220.00
Molecular weight molecular_weight	19929.0 kDa
Excluded volume excluded_volume	24490 Å³
Envelope volume envelope_volume	30035 Å³
Hydration-shell volume shell_volume	14537 Å³
Envelope diameter envelope_diameter	63.9 Å
Shell Rg shell_rg	23.26 Å
Envelope Rg envelope_rg	18.40 Å
Shape Rg shape_rg	18.22 Å
Total Rg total_rg	18.98 Å
Total atoms total_atoms	1403
Residues n_residues	176
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	64.1 Å
Rg (real space) rg_real	19.13 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	8.1930e+06
I(0) uncertainty (real space) i0_real_error	1.0410e+05
Rg (reciprocal space) rg_reciprocal	19.13 Å
I(0) (reciprocal space) i0_reciprocal	8193000.0000
Solution quality estimate total_estimate	0.8908
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.5 Å
Skewness Skewness skewness	0.304
Kurtosis Kurtosis kurtosis	-0.423
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	1153000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.997

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

Unit-cell length a length_a	26.896 Å
Unit-cell length b length_b	89.185 Å
Unit-cell length c length_c	36.290 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.70 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2006
R_work r_work	0.1985
R_free r_free	0.2413

Description description	Carbon dioxide concentrating mechanism protein CcmM
Molecular weight formula_weight	10550.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1500

Crystal Structure of the small subunit-like domain 1 of CcmM from Synechococcus elongatus (strain PCC 7942), thiol-oxidized form

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

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)

来源生物 organism	Synechococcus elongatus (strain PCC 7942)
通用名 common_name	Anacystis nidulans R2
NCBI Class编号 ncbi_taxonomy_id	1140
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	97

fit	/app/data/saxs_computation/hb/6hba/6hba.fit
pddf	/app/data/pr_computation/hb/6hba/6hba.pr.out
profile	/app/data/saxs_computation/hb/6hba/6hba.dat