1cdn

Solution structure of (CD2+)1-calbindin D9K reveals details of the stepwise structural changes along the apo--> (CA2+)II1--> (CA2+)I,II2 binding pathway

Method: SOLUTION NMR Dmax: 34.7 Å Quality: GOOD

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

CALBINDIN D9K

Bos taurus

UniProt P02633

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 4–78 Mutation:INS(MET 1), P43G No other associated polymer SOLUTION NMR mmCIF provides none of the parsed experimental conditions 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.

19 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name S100G_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–76; UniProt 4–78

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 1cdn

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1cdn
Deposition date deposition_date1995-08-04
Structure title titleSolution structure of (CD2+)1-calbindin D9K reveals details of the stepwise structural changes along the apo--> (CA2+)II1--> (CA2+)I,II2 binding pathway
Keywords keywordsEF-HAND, CALCIUM-BINDING PROTEIN; CALCIUM-BINDING PROTEIN
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier11.57
Radius of gyration Rg (electron density) rg_electron11.14
Forward intensity I(0) i0525634000.00
Molecular weight molecular_weight202880.0 kDa
Excluded volume excluded_volume257110 ų
Envelope volume envelope_volume17070 ų
Hydration-shell volume shell_volume11337 ų
Envelope diameter envelope_diameter39.7
Shell Rg shell_rg18.65
Envelope Rg envelope_rg12.92
Shape Rg shape_rg11.11
Total Rg total_rg11.39
Total atoms total_atoms28632
Residues n_residues1800
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 dmax34.7
Rg (real space) rg_real11.45
Rg uncertainty (real space) rg_real_error0.19
I(0) (real space) i0_real5.2560e+08
I(0) uncertainty (real space) i0_real_error5.3240e+06
Rg (reciprocal space) rg_reciprocal11.45
I(0) (reciprocal space) i0_reciprocal525600000.0000
Solution quality estimate total_estimate0.8808
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.3
Skewness Skewness skewness-0.209
Kurtosis Kurtosis kurtosis-0.416
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha61590.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.827; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.995

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1cdna_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.1 — Calbindin D9K

CATH v4.4 (1 domains)

Domain ID domain_id1cdnA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand

8. Citations (4)

9. Files and Curves (10)