1y6w

Trapped intermediate of calmodulin

Method: X-RAY DIFFRACTION Dmax: 71.1 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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–148 Mutation:Q41C, D64N, K75C Non-standard monomer:Yes (specific site not provided by mmCIF) CA CALCIUM ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 TBU TERTIARY-BUTYL ALCOHOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.2;277 K;32% (w/v) 2-methyl-2,4-pentanediol, 10% (v/v) t-butanol, 20 mM Na-cacodylate, 5 mM CaCl2, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.40 Å R-free 0.238

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 1–148; UniProt 1–148

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 1y6w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1y6w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1y6w
Deposition date deposition_date2004-12-07
Structure title titleTrapped intermediate of calmodulin
Keywords keywordsEF-hand, calcium-binding protein, engineered disulfide; Calcium-Binding Protein
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.91
Radius of gyration Rg (electron density) rg_electron20.76
Forward intensity I(0) i06309050.00
Molecular weight molecular_weight17084.0 kDa
Excluded volume excluded_volume20516 ų
Envelope volume envelope_volume25943 ų
Hydration-shell volume shell_volume11710 ų
Envelope diameter envelope_diameter71.2
Shell Rg shell_rg24.48
Envelope Rg envelope_rg20.49
Shape Rg shape_rg20.86
Total Rg total_rg21.03
Total atoms total_atoms1154
Residues n_residues136
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 dmax71.1
Rg (real space) rg_real21.14
Rg uncertainty (real space) rg_real_error0.61
I(0) (real space) i0_real6.3090e+06
I(0) uncertainty (real space) i0_real_error8.5160e+04
Rg (reciprocal space) rg_reciprocal21.10
I(0) (reciprocal space) i0_reciprocal6309000.0000
Solution quality estimate total_estimate0.6159
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary17.5
Skewness Skewness skewness0.436
Kurtosis Kurtosis kurtosis-0.695
Angular range angular_range— – 0.3800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha731200.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.552; Stabil: 1.000; Sysdev: 0.301; Positv: 1.000; Valcen: 0.467; Smooth: 0.979

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1y6wa_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.5 — Calmodulin-like

CATH v4.4 (2 domains)

Domain ID domain_id1y6wA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1y6wA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand

8. Citations (1)

9. Files and Curves (10)