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8e0w

Crystal structure of mouse APCDD1 in P1 space group

Method: X-RAY DIFFRACTION Dmax: 110.1 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein APCDD1

Mus musculus

UniProt Q3U128

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 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
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 × 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

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 8E0W 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 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
8E0R Crystal structure of mouse APCDD1 in P21 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 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
8E0R Crystal structure of mouse APCDD1 in P21 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 × 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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 8e0w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8e0w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8e0w
Deposition date deposition_date2022-08-09
Structure title titleCrystal structure of mouse APCDD1 in P1 space group
Keywords keywordscell signaling protein, beta barrel, lipid binding protein, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.47 Å
Radius of gyration Rg (electron density) rg_electron31.74 Å
Forward intensity I(0) i0157232000.00
Molecular weight molecular_weight96590.0 kDa
Excluded volume excluded_volume119410 ų
Envelope volume envelope_volume154820 ų
Hydration-shell volume shell_volume40615 ų
Envelope diameter envelope_diameter116.6 Å
Shell Rg shell_rg38.59 Å
Envelope Rg envelope_rg31.69 Å
Shape Rg shape_rg31.74 Å
Total Rg total_rg32.29 Å
Total atoms total_atoms6799
Residues n_residues827
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax110.1 Å
Rg (real space) rg_real32.43 Å
Rg uncertainty (real space) rg_real_error0.81 Å
I(0) (real space) i0_real1.5720e+08
I(0) uncertainty (real space) i0_real_error2.4450e+06
Rg (reciprocal space) rg_reciprocal32.45 Å
I(0) (reciprocal space) i0_reciprocal157200000.0000
Solution quality estimate total_estimate0.7093
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.7 Å
Skewness Skewness skewness0.285
Kurtosis Kurtosis kurtosis-0.429
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha46650000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.989; Smooth: 0.957
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)