← Back to search

13go

Crystal Structure of Glycerol Dehydrogenase from Streptococcus agalactiae

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

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	13go
deposition_date	2026-05-05
last_revision	2026-05-13
title	Crystal Structure of Glycerol Dehydrogenase from Streptococcus agalactiae
keywords	Glycerol Dehydrogenase, CSBID, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	41.28 Å
rg_electron	40.90 Å
i0	346456000.00
molecular_weight	154610.0 kDa
excluded_volume	194330 Å³
envelope_volume	253960 Å³
shell_volume	50312 Å³
envelope_diameter	137.5 Å
shell_rg	48.04 Å
envelope_rg	40.20 Å
shape_rg	40.90 Å
total_rg	41.27 Å
total_atoms	10881
n_residues	1447
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	137.1 Å
rg_real	41.21 Å
rg_real_error	1.40 Å
i0_real	3.4650e+08
i0_real_error	6.6170e+06
rg_reciprocal	41.28 Å
i0_reciprocal	346500000.0000
total_estimate	0.8193
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	54.1 Å
skewness	0.155
kurtosis	-0.625
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	30360000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Glycerol dehydrogenase
formula_weight	39183.3 kDa
ec_number	1.1.1.6
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	10915

SNAMKVFASPSRYIQGKDALFQSIEHIKSLGQTPLILCDDVVYNIVGERFLSYLQDDLLPHRVSFNGEASDNEINRVVAVAKEKNSDLIIGLGGGKTIDSAKAIADKVNLPVVIAPTVASTDAPTSALSVIYTDEGAFEKYIFYSKNPDLVLVDTQVIAQAPKRLLASGIADGLATWVEARAVLQKNGIAMAGGRQTLAGVAIAQACERTLFNDSLQALAACDAKVVTKALENVIEANTLLSGLGFESAGLAAAHAIHNGFTALSGDIHHLTHGEKVAYGTLTQLFLENRPKEEIDRYINLYQAIGMPTTLAELHLGDATYEELLKVGQQATIEGETIHEMPFKISAEDVAAALLTVDRYVSNHQ

Source

organism	Streptococcus agalactiae
ncbi_taxonomy_id	1311
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	34

▶

6. Citations (1)

▶

length_a	151.502 Å
length_b	104.360 Å
length_c	104.258 Å
angle_alpha	90.00 °
angle_beta	110.59 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.100 Å
resolution_low	49.660 Å
r_factor	0.2286
r_work	0.2254
r_free	0.2900

fit	/app/data/saxs_computation/3g/13go/13go.fit
pddf	/app/data/pr_computation/3g/13go/13go.pr.out
profile	/app/data/saxs_computation/3g/13go/13go.dat

Crystal Structure of Glycerol Dehydrogenase from Streptococcus agalactiae

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction