2h61

X-ray structure of human Ca2+-loaded S100B

Method: X-RAY DIFFRACTION Dmax: 84.9 Å Quality: EXCELLENT

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

Protein S100-B

Homo sapiens

UniProt P04271

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 0–91 Chain B; UniProt 0–91 Chain C; UniProt 0–91 Chain D; UniProt 0–91 Chain E; UniProt 0–91 Chain F; UniProt 0–91 Chain G; UniProt 0–91 Chain H; UniProt 0–91 Non-standard monomer:Yes (specific site not provided by mmCIF) CA CALCIUM ION × 18 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;289 K;0.1 M HEPES, 18-20%PEG400, 0.2 M CaCl2, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K Resolution 1.90 Å R-free 0.241

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.

14 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name S100B_HUMAN
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 1–92; UniProt 0–91 Author chain B; PDBConstruct 1–92; UniProt 0–91 Author chain E; PDBConstruct 1–92; UniProt 0–91 Author chain F; PDBConstruct 1–92; UniProt 0–91 Author chain H; PDBConstruct 1–92; UniProt 0–91 Author chain C; PDBConstruct 1–92; UniProt 0–91 Author chain D; PDBConstruct 1–92; UniProt 0–91 Author chain G; PDBConstruct 1–92; UniProt 0–91

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 2h61

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2h61
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2h61
Deposition date deposition_date2006-05-30
Structure title titleX-ray structure of human Ca2+-loaded S100B
Keywords keywordsS100, EF-hand, Calcium-binding, RAGE, METAL BINDING PROTEIN, SIGNALING PROTEIN; METAL BINDING PROTEIN, SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.98
Radius of gyration Rg (electron density) rg_electron27.57
Forward intensity I(0) i0122487000.00
Molecular weight molecular_weight85421.0 kDa
Excluded volume excluded_volume105770 ų
Envelope volume envelope_volume131280 ų
Hydration-shell volume shell_volume38114 ų
Envelope diameter envelope_diameter88.0
Shell Rg shell_rg36.23
Envelope Rg envelope_rg27.34
Shape Rg shape_rg27.56
Total Rg total_rg28.44
Total atoms total_atoms5948
Residues n_residues725
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 dmax84.9
Rg (real space) rg_real28.78
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real1.2250e+08
I(0) uncertainty (real space) i0_real_error1.6450e+06
Rg (reciprocal space) rg_reciprocal28.87
I(0) (reciprocal space) i0_reciprocal122500000.0000
Solution quality estimate total_estimate0.9049
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.6
Skewness Skewness skewness0.036
Kurtosis Kurtosis kurtosis-0.492
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13150000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.937

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd2h61a_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd2h61b_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd2h61c_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd2h61d_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd2h61e_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd2h61f_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd2h61g_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd2h61h_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins

CATH v4.4 (8 domains)

Domain ID domain_id2h61A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2h61B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2h61C00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2h61D00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2h61E00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2h61F00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2h61G00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2h61H00
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)