2o72

Crystal Structure Analysis of human E-cadherin (1-213)

Method: X-RAY DIFFRACTION Dmax: 102.0 Å Quality: SUSPICIOUS

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

Epithelial-cadherin

Homo sapiens

UniProt P12830

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 155–367 Fragment:N-Terminal domains 1 and 2, residues 155-317 Mutation:C9S CA CALCIUM ION × 10 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277 K;10% PEG 8000, 0.2M calcium chloride, 5% DMSO, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K, temperature 277K Resolution 2.00 Å R-free 0.234

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.

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CADH1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–213; UniProt 155–367

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 2o72

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2o72
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2o72
Deposition date deposition_date2006-12-09
Structure title titleCrystal Structure Analysis of human E-cadherin (1-213)
Keywords keywordsIg-LIKE DOMAINS, CALCIUM-BINDING PROTEIN, CELL ADHESION, METAL BINDING PROTEIN; CELL ADHESION, METAL BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.40
Radius of gyration Rg (electron density) rg_electron27.94
Forward intensity I(0) i09459230.00
Molecular weight molecular_weight23302.0 kDa
Excluded volume excluded_volume29110 ų
Envelope volume envelope_volume37352 ų
Hydration-shell volume shell_volume13294 ų
Envelope diameter envelope_diameter99.6
Shell Rg shell_rg29.86
Envelope Rg envelope_rg28.32
Shape Rg shape_rg27.90
Total Rg total_rg28.32
Total atoms total_atoms1632
Residues n_residues213
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax102.0
Rg (real space) rg_real28.14
Rg uncertainty (real space) rg_real_error1.31
I(0) (real space) i0_real9.4590e+06
I(0) uncertainty (real space) i0_real_error1.9090e+05
Rg (reciprocal space) rg_reciprocal27.91
I(0) (reciprocal space) i0_reciprocal9458000.0000
Solution quality estimate total_estimate0.4911
Solution quality rating solution_quality SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.6
Skewness Skewness skewness0.651
Kurtosis Kurtosis kurtosis-0.428
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha854700.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.204; Stabil: 1.000; Sysdev: 0.267; Positv: 1.000; Valcen: 0.037; Smooth: 0.932

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2o72a1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.6 — Cadherin-like
Family Family familyb.1.6.1 — Cadherin
Domain ID domain_idd2o72a2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.6 — Cadherin-like
Family Family familyb.1.6.1 — Cadherin

CATH v4.4 (2 domains)

Domain ID domain_id2o72A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id2o72A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins

8. Citations (1)

9. Files and Curves (10)