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1xyd

NMR Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures

Method: SOLUTION NMR Dmax: 53.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

S-100 protein, beta chain

Rattus norvegicus

UniProt P04631

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 0–91 Chain B； UniProt 0–91 Not recorded CA CALCIUM ION × 4 ZN ZINC ION × 2 SOLUTION NMR NMR measurement conditions：pH 7.2；310.15 K；Pressure ambient NMR sample composition：3 mM 15N S100B (monomer concentration), 3 mM Zinc acetate, 10 mM CaCl2, 0.34 mM NaN3, 15 mM NaCl, <0.07 mM DTT, 10 mM TES, 10% D2O NMR sample composition：3 mM 15N,13C S100B (monomer concentration), 3 mM Zinc acetate, 10 mM CaCl2, 0.34 mM NaN3, 15 mM NaCl, <0.07 mM DTT, 10 mM TES, 10% D2O NMR sample composition：1 mM 15N S100B (monomer concentration), 1 mM Zinc acetate, 3.3 mM CaCl2, 0.34 mM NaN3, 15 mM NaCl, <0.07 mM DTT, 10 mM TES, 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.

Other PDB Difference from Current Entry 1XYD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B4C SOLUTION STRUCTURE OF RAT APO-S100B USING DIPOLAR COUPLINGS Deposited 1998-12-17 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–91（91 aa）
Chain B 1–91（91 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 25mM；Pressure 1
Resolution not provided
1DT7 SOLUTION STRUCTURE OF THE C-TERMINAL NEGATIVE REGULATORY DOMAIN OF P53 IN A COMPLEX WITH CA2+-BOUND S100B(BB) Deposited 2000-01-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–92（92 aa） Fragment：BETA CHAIN
Chain B 1–92（92 aa） Fragment：BETA CHAIN
Not recorded CA CALCIUM ION × 4 SOLUTION NMR
NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 25 mM；Pressure ambient
NMR sample composition 3-6 mM S100 (subunit concentration), 0.1 mM EDTA, 0.34 mM NaN3, 5 mM DTT, 17 mM NaCl, 10 mM d11-tris-HCl, 7% D2O, 6-13 mM CaCl2, 4.8-10 mM p53 peptide | 7% D2O, 93% H2O
Resolution not provided
1MWN Solution NMR structure of S100B bound to the high-affinity target peptide TRTK-12 Deposited 2002-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 0–91（92 aa）
Chain B 0–91（92 aa）
Not recorded CA CALCIUM ION × 4 SOLUTION NMR
NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 25 mM；Pressure ambient
NMR sample composition 2.2 mM S100B (subunit concentration), 5.2 mM CaCl2, 2.6 mM TRTK-12 peptide, 10 mM tris-d11, 15 mM NaCl, 0.1 mM EDTA, 5 mM DTT, 0.35 mM NaN3 | 95% H2O/5% D2O
Resolution not provided
1QLK SOLUTION STRUCTURE OF CA(2+)-LOADED RAT S100B (BETABETA) NMR, 20 STRUCTURES Deposited 1997-09-26 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–91（91 aa） Fragment：SUBUNITS A AND B
Chain B 1–91（91 aa） Fragment：SUBUNITS A AND B
Not recorded CA CALCIUM ION × 4 SOLUTION NMR
NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 22mM；Pressure ATMOSPHERIC
NMR sample composition WATER
Resolution not provided
1SYM 3-D SOLUTION STRUCTURE OF REDUCED APO-S100B FROM RAT, NMR, 20 STRUCTURES Deposited 1996-05-29 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–91（91 aa）
Chain B 1–91（91 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2K7O Ca2+-S100B, refined with RDCs Deposited 2008-08-17 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–92（91 aa）
Chain B 2–92（91 aa）
Not recorded CA CALCIUM ION × 4 SOLUTION NMR
NMR measurement conditions pH 6.7；310 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 400 uM [U-15N] S100B, 10 mM CaCl2, 25 mM NaCl, 10 mM [U-99% 2H] MES, pH 6.7, 10 mM DTT, .1 mM NaN3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name S100B_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–92； UniProt 0–91 Author chain B； 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 1xyd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1xyd
Deposition date deposition_date2004-11-09
Structure title titleNMR Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures
Keywords keywordsMetal Binding Protein; METAL BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.83 Å
Radius of gyration Rg (electron density) rg_electron16.35 Å
Forward intensity I(0) i02796690000.00
Molecular weight molecular_weight434980.0 kDa
Excluded volume excluded_volume535570 ų
Envelope volume envelope_volume43787 ų
Hydration-shell volume shell_volume19858 ų
Envelope diameter envelope_diameter61.5 Å
Shell Rg shell_rg24.75 Å
Envelope Rg envelope_rg18.36 Å
Shape Rg shape_rg16.37 Å
Total Rg total_rg16.37 Å
Total atoms total_atoms58600
Residues n_residues3680
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax53.0 Å
Rg (real space) rg_real16.72 Å
Rg uncertainty (real space) rg_real_error0.26 Å
I(0) (real space) i0_real2.7970e+09
I(0) uncertainty (real space) i0_real_error3.3170e+07
Rg (reciprocal space) rg_reciprocal16.74 Å
I(0) (reciprocal space) i0_reciprocal2797000000.0000
Solution quality estimate total_estimate0.8894
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.3 Å
Skewness Skewness skewness0.093
Kurtosis Kurtosis kurtosis-0.383
Angular range angular_range— – 0.4750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha502900.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.927
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1xyda_
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_idd1xydb_
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 (2 domains)

Domain ID domain_id1xydA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xydB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
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8. Citations (1)

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9. Files and Curves (10)