13go

Crystal Structure of Glycerol Dehydrogenase from Streptococcus agalactiae

Method: X-RAY DIFFRACTION Dmax: 137.1 Å Quality: GOOD

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

Glycerol dehydrogenase

Streptococcus agalactiae

UniProt A0A076YVD1

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 1–362 Chain B; UniProt 1–362 Chain C; UniProt 1–362 Chain D; UniProt 1–362 Not recorded EDO 1,2-ETHANEDIOL × 4 ZN ZINC ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;289 K;0.2 M Sodium Chloride, 0.1 M Imidazole:HCl, 1.0 M Ammonium Phosphate Dibasic Resolution 3.10 Å R-free 0.290

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A076YVD1_STRAG
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–365; UniProt 1–362 Author chain B; PDBConstruct 4–365; UniProt 1–362 Author chain C; PDBConstruct 4–365; UniProt 1–362 Author chain D; PDBConstruct 4–365; UniProt 1–362

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 13go

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 13go
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2. Structure Basics 2. Structure Basics

Entry ID entry_id13go
Deposition date deposition_date2026-05-05
最后修订 last_revision2026-05-13
Structure title titleCrystal Structure of Glycerol Dehydrogenase from Streptococcus agalactiae
Keywords keywordsGlycerol Dehydrogenase, CSBID, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier41.28
Radius of gyration Rg (electron density) rg_electron40.90
Forward intensity I(0) i0346456000.00
Molecular weight molecular_weight154610.0 kDa
Excluded volume excluded_volume194330 ų
Envelope volume envelope_volume253960 ų
Hydration-shell volume shell_volume50312 ų
Envelope diameter envelope_diameter137.5
Shell Rg shell_rg48.04
Envelope Rg envelope_rg40.20
Shape Rg shape_rg40.90
Total Rg total_rg41.27
Total atoms total_atoms10881
Residues n_residues1447
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 dmax137.1
Rg (real space) rg_real41.21
Rg uncertainty (real space) rg_real_error1.40
I(0) (real space) i0_real3.4650e+08
I(0) uncertainty (real space) i0_real_error6.6170e+06
Rg (reciprocal space) rg_reciprocal41.28
I(0) (reciprocal space) i0_reciprocal346500000.0000
Solution quality estimate total_estimate0.8193
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.1
Skewness Skewness skewness0.155
Kurtosis Kurtosis kurtosis-0.625
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30360000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)