SAXSdb — 2a18

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

Carbon dioxide concentrating mechanism protein ccmK homolog 4

Synechocystis sp.

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–111 Chain B； UniProt 1–111 Chain C； UniProt 1–111	Not recorded	NH4 AMMONIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M sodium citrate, pH 4.6, 30% PEG 4000, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.28 Å R-free 0.222

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 2A18	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2A10 carboxysome shell protein ccmK4 Deposited 2005-06-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–111（111 aa） Chain B 1–111（111 aa） Chain C 1–111（111 aa） Chain D 1–111（111 aa） Chain E 1–111（111 aa） Chain F 1–111（111 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；293 K；25% ethylene glycol, 20 mM Tris, 100mM NaCl, 10 mM EDTA, 5mM DTT, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.227
3GV2 X-ray Structure of Hexameric HIV-1 CA Deposited 2009-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–110（110 aa） Fragment：UNP residues 133-351 of Capsid protein p24, UNP residues 1-109 of CCMK Chain B 1–110（110 aa） Fragment：UNP residues 133-351 of Capsid protein p24, UNP residues 1-109 of CCMK Chain C 1–110（110 aa） Fragment：UNP residues 133-351 of Capsid protein p24, UNP residues 1-109 of CCMK Chain D 1–110（110 aa） Fragment：UNP residues 133-351 of Capsid protein p24, UNP residues 1-109 of CCMK Chain E 1–110（110 aa） Fragment：UNP residues 133-351 of Capsid protein p24, UNP residues 1-109 of CCMK Chain F 1–110（110 aa） Fragment：UNP residues 133-351 of Capsid protein p24, UNP residues 1-109 of CCMK	Mutation：W184A,M185A Mutation：W184A,M185A Mutation：W184A,M185A Mutation：W184A,M185A Mutation：W184A,M185A Mutation：W184A,M185A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M imidazole, pH 6.5, 600 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 7.00 Å R-free 0.323
6SCR Structure of CcmK4 from Synechocystis sp. PCC6803 Deposited 2019-07-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 3–112（110 aa） Chain B 3–112（110 aa）	Mutation：MAHHHHASGENLYFQGAMA is an added Nterminal tag Mutation：MAHHHHASGENLYFQGAMA is an added Nterminal tag	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；285 K；22 % (w/v) PEG 4000 0.2 M ammonium sulfate 0.1 M sodium acetate at pH 4.6	Resolution 1.80 Å R-free 0.192

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CCMK4_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–112； UniProt 1–111 Author chain B； PDBConstruct 2–112； UniProt 1–111 Author chain C； PDBConstruct 2–112； UniProt 1–111

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	2a18
Deposition date deposition_date	2005-06-18
Structure title title	carboxysome shell protein ccmK4, crystal form 2
Keywords keywords	cyclic hexamer; c6 point symmetry, carboxysome; carboxysome
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.42 Å
Radius of gyration Rg (electron density) rg_electron	21.33 Å
Forward intensity I(0) i0	18583200.00
Molecular weight molecular_weight	33041.0 kDa
Excluded volume excluded_volume	41624 Å³
Envelope volume envelope_volume	49399 Å³
Hydration-shell volume shell_volume	19939 Å³
Envelope diameter envelope_diameter	78.2 Å
Shell Rg shell_rg	27.60 Å
Envelope Rg envelope_rg	21.75 Å
Shape Rg shape_rg	21.33 Å
Total Rg total_rg	22.20 Å
Total atoms total_atoms	2328
Residues n_residues	312
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

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

Maximum dimension Dmax dmax	76.2 Å
Rg (real space) rg_real	22.49 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.8580e+07
I(0) uncertainty (real space) i0_real_error	2.5480e+05
Rg (reciprocal space) rg_reciprocal	22.47 Å
I(0) (reciprocal space) i0_reciprocal	18580000.0000
Solution quality estimate total_estimate	0.6911
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.429
Kurtosis Kurtosis kurtosis	-0.304
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3656000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 0.189; Positv: 1.000; Valcen: 0.945; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Carbon dioxide concentrating mechanism protein ccmK homolog 4
Molecular weight formula_weight	13454.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2408

MSAQSAVGSIETIGFPGILAAADAMVKAGRITIVGYIRAGSARFTLNIRGDVQEVKTAMAAGIDAINRTEGADVKTWVIIPRPHENVVAVLPIDFSPEVEPFREAAEGLNRRGVPRGLEHHHHHH

来源 Source

来源生物 organism	Synechocystis sp.
NCBI Class编号 ncbi_taxonomy_id	1148
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	AMMONIUM ION
Molecular weight formula_weight	18.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	80

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2a18a_
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	d2a18b_
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	d2a18c_
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

CATH v4.4 (3 domains)

Domain ID domain_id	2a18A00
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	2a18B00
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	2a18C00
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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8. Citations (1)

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Unit-cell length a length_a	70.549 Å
Unit-cell length b length_b	125.040 Å
Unit-cell length c length_c	32.521 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	12

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.280 Å
Low-resolution limit resolution_low	62.500 Å
R factor r_factor	0.2036
R_work r_work	0.2026
R_free r_free	0.2224

fit	/app/data/saxs_computation/a1/2a18/2a18.fit
pddf	/app/data/pr_computation/a1/2a18/2a18.pr.out
profile	/app/data/saxs_computation/a1/2a18/2a18.dat

carboxysome shell protein ccmK4, crystal form 2

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

Carbon dioxide concentrating mechanism protein ccmK homolog 4

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