SAXSdb — 1c3h

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

30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR

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 111–247 Chain B； UniProt 111–247 Chain C； UniProt 111–247	Not recorded	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 111–247 Chain E； UniProt 111–247 Chain F； UniProt 111–247	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

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 1C3H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C28 THE CRYSTAL STRUCTURE OF A COMPLMENT-1Q FAMILY PROTEIN SUGGESTS AN EVOLUTIONARY LINK TO TUMOR NECROSIS FACTOR Deposited 1999-07-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 113–247（135 aa） Chain B 113–247（135 aa） Chain C 113–247（135 aa）	Not recorded	No recorded non-water small molecule	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

1 other PDB entries and 1 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 1–137； UniProt 111–247 Author chain B； PDBConstruct 1–137； UniProt 111–247 Author chain C； PDBConstruct 1–137； UniProt 111–247 Author chain D； PDBConstruct 1–137； UniProt 111–247 Author chain E； PDBConstruct 1–137； UniProt 111–247 Author chain F； PDBConstruct 1–137； UniProt 111–247

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	1c3h
Deposition date deposition_date	1999-07-27
Structure title title	ACRP30 CALCIUM COMPLEX
Keywords keywords	ACRP30 C1Q TNF TRIMER ALL-BETA CALCIUM-BOUND, SIGNALING PROTEIN; SIGNALING 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	43.99 Å
Radius of gyration Rg (electron density) rg_electron	43.78 Å
Forward intensity I(0) i0	123852000.00
Molecular weight molecular_weight	94128.0 kDa
Excluded volume excluded_volume	118160 Å³
Envelope volume envelope_volume	159480 Å³
Hydration-shell volume shell_volume	29610 Å³
Envelope diameter envelope_diameter	141.7 Å
Shell Rg shell_rg	51.31 Å
Envelope Rg envelope_rg	41.91 Å
Shape Rg shape_rg	43.76 Å
Total Rg total_rg	44.19 Å
Total atoms total_atoms	6674
Residues n_residues	822
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	143.0 Å
Rg (real space) rg_real	44.39 Å
Rg uncertainty (real space) rg_real_error	1.88 Å
I(0) (real space) i0_real	1.2390e+08
I(0) uncertainty (real space) i0_real_error	2.4830e+06
Rg (reciprocal space) rg_reciprocal	44.00 Å
I(0) (reciprocal space) i0_reciprocal	123800000.0000
Solution quality estimate total_estimate	0.6230
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.210
Kurtosis Kurtosis kurtosis	-1.309
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	94600000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.009; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.157; Smooth: 0.911

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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	30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR
Molecular weight formula_weight	15860.7 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	7182

AYMYRSAFSVGLETRVTVPNVPIRFTKIFYNQQNHYDGSTGKFYCNIPGLYYFSYHITVYMKDVKVSLFKKDKAVLFTYDQYQEKNVDQASGSVLLHLEVGDQVWLQVYGDGDHNGLYADNVNDSTFTGFLLYHDTN

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 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	508

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1c3ha_
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	d1c3hb_
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	d1c3hc_
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	d1c3hd_
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	d1c3he_
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	d1c3hf_
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 (6 domains)

Domain ID domain_id	1c3hA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1c3hB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1c3hC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1c3hD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1c3hE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1c3hF00
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	58.639 Å
Unit-cell length b length_b	58.711 Å
Unit-cell length c length_c	87.315 Å
Unit-cell angle α angle_alpha	70.55 °
Unit-cell angle β angle_beta	70.62 °
Unit-cell angle γ angle_gamma	60.14 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2480

fit	/app/data/saxs_computation/c3/1c3h/1c3h.fit
pddf	/app/data/pr_computation/c3/1c3h/1c3h.pr.out
profile	/app/data/saxs_computation/c3/1c3h/1c3h.dat

ACRP30 CALCIUM COMPLEX

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

30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR

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