SAXSdb — 1a6d

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

THERMOSOME (ALPHA SUBUNIT)

OrganismNot specified

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 heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain A； UniProt 1–545	Not recorded	THERMOSOME (BETA SUBUNIT) × 8 （P48425）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；pH 5.6	Resolution 2.60 Å R-free 0.298
2	Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1–545	Not recorded	THERMOSOME (BETA SUBUNIT) × 4 （P48425）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；pH 5.6	Resolution 2.60 Å R-free 0.298

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 1A6D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A6E THERMOSOME-MG-ADP-ALF3 COMPLEX Deposited 1998-02-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–545（545 aa）	Not recorded	MG MAGNESIUM ION × 16 ADP ADENOSINE-5'-DIPHOSPHATE × 16 AF3 ALUMINUM FLUORIDE × 16	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 3.20 Å R-free 0.285
1A6E THERMOSOME-MG-ADP-ALF3 COMPLEX Deposited 1998-02-24	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–545（545 aa）	Not recorded	MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 8 AF3 ALUMINUM FLUORIDE × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 3.20 Å R-free 0.285
1ASS APICAL DOMAIN OF THE CHAPERONIN FROM THERMOPLASMA ACIDOPHILUM Deposited 1997-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 214–365（152 aa） Fragment：ALPHA-SUBUNIT, APICAL DOMAIN, SUBSTRATE-BINDING DOMAIN	Not recorded	NA SODIUM ION × 2 PO4 PHOSPHATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.5；pH 3.5	Resolution 2.30 Å R-free 0.251
1ASX APICAL DOMAIN OF THE CHAPERONIN FROM THERMOPLASMA ACIDOPHILUM Deposited 1997-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 214–365（152 aa） Fragment：ALPHA SUBUNIT, APICAL DOMAIN, SUBSTRATE-BINDING DOMAIN	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.5；pH 3.5	Resolution 2.80 Å R-free 0.272

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	THSA_THEAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–545； UniProt 1–545

THERMOSOME (BETA SUBUNIT)

OrganismNot specified

UniProt P48425

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 heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain B； UniProt 1–543	Not recorded	THERMOSOME (ALPHA SUBUNIT) × 8 （P48424）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；pH 5.6	Resolution 2.60 Å R-free 0.298
2	Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain B； UniProt 1–543	Not recorded	THERMOSOME (ALPHA SUBUNIT) × 4 （P48424）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；pH 5.6	Resolution 2.60 Å R-free 0.298

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 1A6D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A6E THERMOSOME-MG-ADP-ALF3 COMPLEX Deposited 1998-02-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain B 1–543（543 aa）	Not recorded	MG MAGNESIUM ION × 16 ADP ADENOSINE-5'-DIPHOSPHATE × 16 AF3 ALUMINUM FLUORIDE × 16	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 3.20 Å R-free 0.285
1A6E THERMOSOME-MG-ADP-ALF3 COMPLEX Deposited 1998-02-24	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–543（543 aa）	Not recorded	MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 8 AF3 ALUMINUM FLUORIDE × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 3.20 Å R-free 0.285
1E0R Beta-apical domain of thermosome Deposited 2000-04-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 214–367（154 aa） Fragment：SUBSTRATE-BINDING DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.1；pH 9.10	Resolution 2.80 Å R-free 0.318

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

View Construct and Data Evidence

UniProt name	THSB_THEAC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–543； UniProt 1–543

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	1a6d
Deposition date deposition_date	1998-02-24
Structure title title	THERMOSOME FROM T. ACIDOPHILUM
Keywords keywords	THERMOPLASMA ACIDOPHILUM, GROUP II CHAPERONIN, CCT, TRIC, PROTEIN FOLDING, ATPASE, CHAPERONIN; CHAPERONIN
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	35.21 Å
Radius of gyration Rg (electron density) rg_electron	34.72 Å
Forward intensity I(0) i0	183166000.00
Molecular weight molecular_weight	108270.0 kDa
Excluded volume excluded_volume	135830 Å³
Envelope volume envelope_volume	180140 Å³
Hydration-shell volume shell_volume	43762 Å³
Envelope diameter envelope_diameter	115.6 Å
Shell Rg shell_rg	40.87 Å
Envelope Rg envelope_rg	34.09 Å
Shape Rg shape_rg	34.74 Å
Total Rg total_rg	35.14 Å
Total atoms total_atoms	9324
Residues n_residues	1005
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	115.3 Å
Rg (real space) rg_real	35.18 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.8320e+08
I(0) uncertainty (real space) i0_real_error	2.9030e+06
Rg (reciprocal space) rg_reciprocal	35.20 Å
I(0) (reciprocal space) i0_reciprocal	183200000.0000
Solution quality estimate total_estimate	0.8998
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.5 Å
Skewness Skewness skewness	0.251
Kurtosis Kurtosis kurtosis	-0.539
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	33250000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.923

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	THERMOSOME (ALPHA SUBUNIT)
Molecular weight formula_weight	58323.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9324

MMTGQVPILVLKEGTQREQGKNAQRNNIEAAKAIADAVRTTLGPKGMDKMLVDSIGDIIISNDGATILKEMDVEHPTAKMIVEVSKAQDTAVGDGTTTAVVLSGELLKQAETLLDQGVHPTVISNGYRLAVNEARKIIDEIAEKSTDDATLRKIALTALSGKNTGLSNDFLADLVVKAVNAVAEVRDGKTIVDTANIKVDKKNGGSVNDTQFISGIVIDKEKVHSKMPDVVKNAKIALIDSALEIKKTEIEAKVQISDPSKIQDFLNQETNTFKQMVEKIKKSGANVVLCQKGIDDVAQHYLAKEGIYAVRRVKKSDMEKLAKATGAKIVTDLDDLTPSVLGEAETVEERKIGDDRMTFVMGCKNPKAVSILIRGGTDHVVSEVERALNDAIRVVAITKEDGKFLWGGGAVEAELAMRLAKYANSVGGREQLAIEAFAKALEIIPRTLAENAGIDPINTLIKLKADDEKGRISVGVDLDNNGVGDMKAKGVVDPLRVKTHALESAVEVATMILRIDDVIASKKSTPPSGQGGQGQGMPGGGMPEY

Entity 2 Entity 2 polymer

Description description	THERMOSOME (BETA SUBUNIT)
Molecular weight formula_weight	58552.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MIAGQPIFILKEGTKRESGKDAMKENIEAAIAISNSVRSSLGPRGMDKMLVDSLGDIVITNDGVTILKEMDVEHPAAKMMVEVSKTQDSFVGDGTTTAVIIAGGLLQQAQGLINQNVHPTVISEGYRMASEEAKRVIDEISTKIGADEKALLLKMAQTSLNSKSASVAKDKLAEISYEAVKSVAELRDGKYYVDFDNIQVVKKQGGAIDDTQLINGIIVDKEKVHPGMPDVVKDAKIALLDAPLEIKKPEFDTNLRIEDPSMIQKFLAQEENMLREMVDKIKSVGANVVITQKGIDDMAQHYLSRAGIYAVRRVKKSDMDKLAKATGASIVSTIDEISSSDLGTAERVEQVKVGEDYMTFVTGCKNPKAVSILVRGETEHVVDEMERSITDSLHVVASALEDGAYAAGGGATAAEIAFRLRSYAQKIGGRQQLAIEKFADAIEEIPRALAENAGLDPIDILLKLRAEHAKGNKTYGINVFTGEIEDMVKNGVIEPIRVGKQAIESATEAAIMILRIDDVIATKSSSSSSNPPKSGSSSESSED

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1a6da1
Class class	a — All alpha proteins
Fold Fold fold	a.129 — GroEL equatorial domain-like
Superfamily Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
Family Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

Domain ID domain_id	d1a6da2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

Domain ID domain_id	d1a6da3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.56 — GroEL-intermediate domain like
Superfamily Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
Family Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

Domain ID domain_id	d1a6db1
Class class	a — All alpha proteins
Fold Fold fold	a.129 — GroEL equatorial domain-like
Superfamily Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
Family Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

Domain ID domain_id	d1a6db2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

Domain ID domain_id	d1a6db3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.56 — GroEL-intermediate domain like
Superfamily Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
Family Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

CATH v4.4 (6 domains)

Domain ID domain_id	1a6dA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	1a6dA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	1a6dA03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

Domain ID domain_id	1a6dB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	1a6dB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	1a6dB03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

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8. Citations (1)

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Unit-cell length a length_a	168.300 Å
Unit-cell length b length_b	168.300 Å
Unit-cell length c length_c	203.400 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	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2150
R_work r_work	0.2150
R_free r_free	0.2980

fit	/app/data/saxs_computation/a6/1a6d/1a6d.fit
pddf	/app/data/pr_computation/a6/1a6d/1a6d.pr.out
profile	/app/data/saxs_computation/a6/1a6d/1a6d.dat

THERMOSOME FROM T. ACIDOPHILUM

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

THERMOSOME (ALPHA SUBUNIT)

State in the Current Structure

Other States of the Same Protein in the Database

THERMOSOME (BETA SUBUNIT)

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

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)