SAXSdb — 1d8s

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer 蛋白 3 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: trimeric	Entity 1：F1 ATPASE (ALPHA SUBUNIT) × 1 Entity 2：F1 ATPASE (BETA SUBUNIT) × 1 Entity 3：F1 ATPASE (GAMMA SUBUNIT) × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；Tris, PEG 8000, glycerol, NaCl, MgSO4, LiSO4, NaN3, EDTA, AMP-PNP, ATP, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 4.40 Å
2	Protein heterocomplex Heteromer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：F1 ATPASE (ALPHA SUBUNIT) × 1 Entity 2：F1 ATPASE (BETA SUBUNIT) × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；Tris, PEG 8000, glycerol, NaCl, MgSO4, LiSO4, NaN3, EDTA, AMP-PNP, ATP, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 4.40 Å
3	Protein heterocomplex Heteromer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：F1 ATPASE (ALPHA SUBUNIT) × 1 Entity 2：F1 ATPASE (BETA SUBUNIT) × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；Tris, PEG 8000, glycerol, NaCl, MgSO4, LiSO4, NaN3, EDTA, AMP-PNP, ATP, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 4.40 Å

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	1d8s
Deposition date deposition_date	1999-10-25
Structure title title	ESCHERICHIA COLI F1 ATPASE
Keywords keywords	HYDROLASE; HYDROLASE
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	43.02 Å
Radius of gyration Rg (electron density) rg_electron	42.46 Å
Forward intensity I(0) i0	1154570000.00
Molecular weight molecular_weight	172200.0 kDa
Excluded volume excluded_volume	169190 Å³
Envelope volume envelope_volume	434420 Å³
Hydration-shell volume shell_volume	84094 Å³
Envelope diameter envelope_diameter	157.3 Å
Shell Rg shell_rg	49.58 Å
Envelope Rg envelope_rg	40.43 Å
Shape Rg shape_rg	42.44 Å
Total Rg total_rg	42.79 Å
Total atoms total_atoms	12282
Residues n_residues	3070
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	136.7 Å
Rg (real space) rg_real	42.73 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	1.1550e+09
I(0) uncertainty (real space) i0_real_error	1.9040e+07
Rg (reciprocal space) rg_reciprocal	43.02 Å
I(0) (reciprocal space) i0_reciprocal	1155000000.0000
Solution quality estimate total_estimate	0.8795
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	55.4 Å
Skewness Skewness skewness	0.095
Kurtosis Kurtosis kurtosis	-0.411
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	212600000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.943

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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	F1 ATPASE (ALPHA SUBUNIT)
Molecular weight formula_weight	41889.6 kDa
EC 编号 ec_number	3.6.1.34
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	12283

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来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	F1 ATPASE (BETA SUBUNIT)
Molecular weight formula_weight	39762.0 kDa
EC 编号 ec_number	3.6.1.34
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

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来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	F1 ATPASE (GAMMA SUBUNIT)
Molecular weight formula_weight	18230.4 kDa
EC 编号 ec_number	3.6.1.34
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

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来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d1d8sa_
Class class	i — Low resolution protein structures
Fold Fold fold	i.3 — ATP synthase
Superfamily Superfamily superfamily	i.3.1 — ATP synthase
Family Family family	i.3.1.1 — ATP synthase

Domain ID domain_id	d1d8sb_
Class class	i — Low resolution protein structures
Fold Fold fold	i.3 — ATP synthase
Superfamily Superfamily superfamily	i.3.1 — ATP synthase
Family Family family	i.3.1.1 — ATP synthase

Domain ID domain_id	d1d8sc_
Class class	i — Low resolution protein structures
Fold Fold fold	i.3 — ATP synthase
Superfamily Superfamily superfamily	i.3.1 — ATP synthase
Family Family family	i.3.1.1 — ATP synthase

Domain ID domain_id	d1d8sd_
Class class	i — Low resolution protein structures
Fold Fold fold	i.3 — ATP synthase
Superfamily Superfamily superfamily	i.3.1 — ATP synthase
Family Family family	i.3.1.1 — ATP synthase

Domain ID domain_id	d1d8se_
Class class	i — Low resolution protein structures
Fold Fold fold	i.3 — ATP synthase
Superfamily Superfamily superfamily	i.3.1 — ATP synthase
Family Family family	i.3.1.1 — ATP synthase

Domain ID domain_id	d1d8sf_
Class class	i — Low resolution protein structures
Fold Fold fold	i.3 — ATP synthase
Superfamily Superfamily superfamily	i.3.1 — ATP synthase
Family Family family	i.3.1.1 — ATP synthase

Domain ID domain_id	d1d8sg_
Class class	i — Low resolution protein structures
Fold Fold fold	i.3 — ATP synthase
Superfamily Superfamily superfamily	i.3.1 — ATP synthase
Family Family family	i.3.1.1 — ATP synthase

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8. Citations (2)

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Unit-cell length a length_a	180.680 Å
Unit-cell length b length_b	197.520 Å
Unit-cell length c length_c	237.900 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	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	4.400 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/d8/1d8s/1d8s.fit
pddf	/app/data/pr_computation/d8/1d8s/1d8s.pr.out
profile	/app/data/saxs_computation/d8/1d8s/1d8s.dat

ESCHERICHIA COLI F1 ATPASE

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

Assembly Composition of the Current Entry

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (7 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)