2lgf

Solution structure of Ca2+/calmodulin complexed with a peptide representing the calmodulin-binding domain of L-selectin

Method: SOLUTION NMR Dmax: 50.9 Å Quality: REASONABLE

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

Calmodulin

Homo sapiens

UniProt P62158

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 3–149 Fragment:sequence database residues 4-149 L-selectin × 1 (P14151) CA CALCIUM ION × 4 SOLUTION NMR NMR measurement conditions:pH 6.8;303 K;Ionic strength (raw mmCIF value) 0.1;Pressure ambient NMR measurement conditions:pH 6.8;303 K;Ionic strength (raw mmCIF value) 0.3;Pressure ambient NMR sample composition:0.5-0.8 mM [U-13C; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.5-0.8 mM [U-2H; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.5-0.8 mM [1H/13C-methyl Met; U-2H; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 100% D2O | 100% D2O NMR sample composition:0.5-0.8 mM [U-13C; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 300 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.5-0.8 mM [U-13C; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 300 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 16 w/v Pf1 phage, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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.

105 other PDB entries and 176 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CALM_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–147; UniProt 3–149

L-selectin

OrganismNot specified

UniProt P14151

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 349–363 Fragment:sequence database residues 349-363 Calmodulin × 1 (P62158) CA CALCIUM ION × 4 SOLUTION NMR NMR measurement conditions:pH 6.8;303 K;Ionic strength (raw mmCIF value) 0.1;Pressure ambient NMR measurement conditions:pH 6.8;303 K;Ionic strength (raw mmCIF value) 0.3;Pressure ambient NMR sample composition:0.5-0.8 mM [U-13C; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.5-0.8 mM [U-2H; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.5-0.8 mM [1H/13C-methyl Met; U-2H; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 100% D2O | 100% D2O NMR sample composition:0.5-0.8 mM [U-13C; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 300 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.5-0.8 mM [U-13C; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 300 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 16 w/v Pf1 phage, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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.

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

View Construct and Data Evidence
UniProt name LYAM1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–15; UniProt 349–363

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 2lgf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2lgf
Deposition date deposition_date2011-07-25
Structure title titleSolution structure of Ca2+/calmodulin complexed with a peptide representing the calmodulin-binding domain of L-selectin
Keywords keywordsMETAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier16.83
Radius of gyration Rg (electron density) rg_electron15.37
Forward intensity I(0) i06958490.00
Molecular weight molecular_weight18492.0 kDa
Excluded volume excluded_volume22837 ų
Envelope volume envelope_volume26462 ų
Hydration-shell volume shell_volume14562 ų
Envelope diameter envelope_diameter50.0
Shell Rg shell_rg21.25
Envelope Rg envelope_rg15.47
Shape Rg shape_rg15.38
Total Rg total_rg16.40
Total atoms total_atoms2528
Residues n_residues161
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 dmax50.9
Rg (real space) rg_real16.72
Rg uncertainty (real space) rg_real_error0.25
I(0) (real space) i0_real6.9580e+06
I(0) uncertainty (real space) i0_real_error8.2440e+04
Rg (reciprocal space) rg_reciprocal16.73
I(0) (reciprocal space) i0_reciprocal6959000.0000
Solution quality estimate total_estimate0.7328
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.8
Skewness Skewness skewness0.082
Kurtosis Kurtosis kurtosis-0.411
Angular range angular_range— – 0.4750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha770500.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 0.272; Positv: 1.000; Valcen: 0.980; Smooth: 0.976

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)