SAXSdb — 1c28

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

PROTEIN (30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR (ACRP30))

Mus musculus

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 113–247 Chain B； UniProt 113–247 Chain C； UniProt 113–247	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；1.8% PEG 4K, 0.1M BIS-TRIS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4.0K	Resolution 2.10 Å R-free 0.276

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 1C28	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C3H ACRP30 CALCIUM COMPLEX Deposited 1999-07-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 111–247（137 aa） Chain B 111–247（137 aa） Chain C 111–247（137 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M BIS-TRIS, 20MM CACL2, 2% PEG 4K, -- CRYO: 15% ETHYLENE GLYCOL, 19% SUCROSE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4CK, temperature 277K	Resolution 2.10 Å R-free 0.248
1C3H ACRP30 CALCIUM COMPLEX Deposited 1999-07-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 111–247（137 aa） Chain E 111–247（137 aa） Chain F 111–247（137 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M BIS-TRIS, 20MM CACL2, 2% PEG 4K, -- CRYO: 15% ETHYLENE GLYCOL, 19% SUCROSE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4CK, temperature 277K	Resolution 2.10 Å R-free 0.248

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

View Construct and Data Evidence

UniProt name	ADIPO_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–135； UniProt 113–247 Author chain B； PDBConstruct 1–135； UniProt 113–247 Author chain C； PDBConstruct 1–135； UniProt 113–247

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	1c28
Deposition date deposition_date	1999-07-22
Structure title title	THE CRYSTAL STRUCTURE OF A COMPLMENT-1Q FAMILY PROTEIN SUGGESTS AN EVOLUTIONARY LINK TO TUMOR NECROSIS FACTOR
Keywords keywords	ACRP30 C1Q TNF TRIMER ALL-BETA, SERUM PROTEIN; SERUM PROTEIN
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	19.98 Å
Radius of gyration Rg (electron density) rg_electron	18.65 Å
Forward intensity I(0) i0	22985900.00
Molecular weight molecular_weight	38584.0 kDa
Excluded volume excluded_volume	48885 Å³
Envelope volume envelope_volume	53615 Å³
Hydration-shell volume shell_volume	22943 Å³
Envelope diameter envelope_diameter	59.2 Å
Shell Rg shell_rg	25.98 Å
Envelope Rg envelope_rg	18.91 Å
Shape Rg shape_rg	18.62 Å
Total Rg total_rg	19.74 Å
Total atoms total_atoms	2743
Residues n_residues	338
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	58.5 Å
Rg (real space) rg_real	19.81 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	2.2990e+07
I(0) uncertainty (real space) i0_real_error	3.2190e+05
Rg (reciprocal space) rg_reciprocal	19.84 Å
I(0) (reciprocal space) i0_reciprocal	22990000.0000
Solution quality estimate total_estimate	0.9050
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.011
Kurtosis Kurtosis kurtosis	-0.552
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7316000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.979

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1c28a_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d1c28b_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d1c28c_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

CATH v4.4 (3 domains)

Domain ID domain_id	1c28A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1c28B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1c28C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Unit-cell length a length_a	112.300 Å
Unit-cell length b length_b	112.300 Å
Unit-cell length c length_c	71.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2760

Description description	PROTEIN (30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR (ACRP30))
Molecular weight formula_weight	15626.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3132

THE CRYSTAL STRUCTURE OF A COMPLMENT-1Q FAMILY PROTEIN SUGGESTS AN EVOLUTIONARY LINK TO TUMOR NECROSIS FACTOR

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

PROTEIN (30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR (ACRP30))

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

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
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	389

fit	/app/data/saxs_computation/c2/1c28/1c28.fit
pddf	/app/data/pr_computation/c2/1c28/1c28.pr.out
profile	/app/data/saxs_computation/c2/1c28/1c28.dat