SAXSdb — 8e0r

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

Protein APCDD1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 27–482	Fragment：extracellular domain (UNP residues 27-482)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；0.7 M magnesium formate, 0.1 M Bis-Tris propane, pH 7.0	Resolution 1.95 Å R-free 0.247
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 27–482	Fragment：extracellular domain (UNP residues 27-482)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；0.7 M magnesium formate, 0.1 M Bis-Tris propane, pH 7.0	Resolution 1.95 Å R-free 0.247

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 8E0R	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8E0P Crystal structure of mouse APCDD1 in fusion with engineered MBP Deposited 2022-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 46–482（437 aa）	Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PLM PALMITIC ACID × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol	Resolution 2.33 Å R-free 0.239
8E0P Crystal structure of mouse APCDD1 in fusion with engineered MBP Deposited 2022-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 46–482（437 aa）	Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol	Resolution 2.33 Å R-free 0.239
8E0P Crystal structure of mouse APCDD1 in fusion with engineered MBP Deposited 2022-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 46–482（437 aa）	Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PLM PALMITIC ACID × 1 GOL GLYCEROL × 1 DMX 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol	Resolution 2.33 Å R-free 0.239
8E0P Crystal structure of mouse APCDD1 in fusion with engineered MBP Deposited 2022-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 46–482（437 aa）	Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 DMX 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol	Resolution 2.33 Å R-free 0.239
8E0W Crystal structure of mouse APCDD1 in P1 space group Deposited 2022-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–482（456 aa） Fragment：extracellular domain (UNP residues 27-482)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.8；293 K；0.1 M magnesium acetate, 0.1 M sodium citrate, pH 5.8, 14% PEG5000 MME	Resolution 2.15 Å R-free 0.220
8E0W Crystal structure of mouse APCDD1 in P1 space group Deposited 2022-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–482（456 aa） Fragment：extracellular domain (UNP residues 27-482)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.8；293 K；0.1 M magnesium acetate, 0.1 M sodium citrate, pH 5.8, 14% PEG5000 MME	Resolution 2.15 Å R-free 0.220

2 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	APCD1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–459； UniProt 27–482 Author chain B； PDBConstruct 4–459； UniProt 27–482

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	8e0r
Deposition date deposition_date	2022-08-09
Structure title title	Crystal structure of mouse APCDD1 in P21 space group
Keywords keywords	cell signaling protein, beta barrel, lipid binding protein, 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	32.00 Å
Radius of gyration Rg (electron density) rg_electron	31.43 Å
Forward intensity I(0) i0	152253000.00
Molecular weight molecular_weight	95431.0 kDa
Excluded volume excluded_volume	118230 Å³
Envelope volume envelope_volume	154360 Å³
Hydration-shell volume shell_volume	41015 Å³
Envelope diameter envelope_diameter	115.7 Å
Shell Rg shell_rg	38.26 Å
Envelope Rg envelope_rg	31.52 Å
Shape Rg shape_rg	31.44 Å
Total Rg total_rg	31.98 Å
Total atoms total_atoms	6726
Residues n_residues	823
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	108.5 Å
Rg (real space) rg_real	31.98 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	1.5230e+08
I(0) uncertainty (real space) i0_real_error	2.6320e+06
Rg (reciprocal space) rg_reciprocal	32.00 Å
I(0) (reciprocal space) i0_reciprocal	152300000.0000
Solution quality estimate total_estimate	0.8847
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.2 Å
Skewness Skewness skewness	0.317
Kurtosis Kurtosis kurtosis	-0.401
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	55380000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.981

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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	Protein APCDD1
Molecular weight formula_weight	53771.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7140

ETGLLHPDSRSHPRSLEKSAWRAFKESQCHHMLKHLHNGARITVQMPPTIEGHWVSTGCEVRSGPEFMTRSYRFYNNNTFKAYQFYYGSNRCTNPTYTLIIRGKIRLRQASWIIRGGTEADYQLHGVQVICHTEAVAEQLSRLVNRTCPGFLAPGGPWVQDVAYDLWQEESNHECTKAVNFAMHELQLIRVEKQYPHHSLDHLVEELFLGDIHTDATQRVFYRPSSYQPPLQNAKNHNHACIACRIIFRSDEHHPPILPPKADLTIGLHGEWVSQRCEVRPEVLFLTRHFIFHDNNNTWEGHYYHYSDPVCKHPTFTIYARGRYSRGVLSSKVMGGTEFVFKVNHMKVTPMDAATASLLNVFSGNECGAEGSWQVGIQQDVTHTNGCVALGIKLPHTEYEIFKMEQDTRGRYLLFNGQRPSDGSSPDRPEKRATSYQMPLVQCASSSPRAEELLEDSQGTHHHHHHHH

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	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	374

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8. Citations (1)

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Unit-cell length a length_a	49.861 Å
Unit-cell length b length_b	144.128 Å
Unit-cell length c length_c	64.381 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.52 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	34.000 Å
R factor r_factor	0.2111
R_work r_work	0.2092
R_free r_free	0.2471

fit	/app/data/saxs_computation/e0/8e0r/8e0r.fit
pddf	/app/data/pr_computation/e0/8e0r/8e0r.pr.out
profile	/app/data/saxs_computation/e0/8e0r/8e0r.dat

Crystal structure of mouse APCDD1 in P21 space group

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

Protein APCDD1

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