← Back to search

13gn

Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis in complex with SN-GLYCEROL-1-PHOSPHATE

Method: X-RAY DIFFRACTION D_max: 124.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	13gn
deposition_date	2026-05-05
last_revision	2026-05-20
title	Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis in complex with SN-GLYCEROL-1-PHOSPHATE
keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, L-erythrulose-1-phosphate isomerase, Brucella melitensis, Isomerase ;; ISOMERASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	35.14 Å
rg_electron	34.80 Å
i0	173502000.00
molecular_weight	105470.0 kDa
excluded_volume	131820 Å³
envelope_volume	159100 Å³
shell_volume	39578 Å³
envelope_diameter	123.9 Å
shell_rg	39.28 Å
envelope_rg	34.75 Å
shape_rg	34.80 Å
total_rg	35.10 Å
total_atoms	7410
n_residues	969
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	124.9 Å
rg_real	35.34 Å
rg_real_error	1.32 Å
i0_real	1.7350e+08
i0_real_error	3.1810e+06
rg_reciprocal	35.22 Å
i0_reciprocal	173500000.0000
total_estimate	0.8430
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	33.3 Å
skewness	0.494
kurtosis	-0.220
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	59780000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.741; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; Smooth: 0.892

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	L-erythrulose-1-phosphate isomerase
formula_weight	28744.6 kDa
ec_number	5.3.1.33
mutation	A173D
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8026

MAHHHHHHKFWIGTSWKMNKTLAEARLFAEALKAADAGRSPDIQRFVIPPFTAVREVKEILSGTSVKVGAQNMHWADQGAWTGEISPLMLKDCNLDIVELGHSERREHFGETNETVGLKVEAAVRHGLIPLICIGETLEDRESGRAAAVLEEEVRGALSKLSEAQKQAEILFAYEPVWDIGENGIPASADYADARQAEIIAVAQSVLARRVPCLYGGSVNPGNCEELIACPHIDGLFIGRSAWNVEGYLDILARCATKVQAN

Source

organism	Brucella abortus 2308
ncbi_taxonomy_id	359391
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	SN-GLYCEROL-1-PHOSPHATE
formula_weight	172.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	573

▶

6. Citations (1)

▶

length_a	45.802 Å
length_b	49.525 Å
length_c	104.793 Å
angle_alpha	92.72 °
angle_beta	96.10 °
angle_gamma	93.72 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.950 Å
resolution_low	45.560 Å
r_factor	0.1650
r_work	0.1622
r_free	0.2163

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