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9pyv

Crystal structure of Uracil-DNA glycosylase from Burkholderia thailandensis

Method: X-RAY DIFFRACTION D_max: 57.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pyv
deposition_date	2025-08-08
last_revision	2025-08-20
title	Crystal structure of Uracil-DNA glycosylase from Burkholderia thailandensis
keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, Uracil-DNA glycosylase, Burkholderia thailandensis, ISOMERASE, HYDROLASE ;; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	18.71 Å
rg_electron	17.18 Å
i0	14163900.00
molecular_weight	26935.0 kDa
excluded_volume	33083 Å³
envelope_volume	37896 Å³
shell_volume	18196 Å³
envelope_diameter	56.8 Å
shell_rg	23.62 Å
envelope_rg	17.38 Å
shape_rg	17.13 Å
total_rg	18.22 Å
total_atoms	1888
n_residues	235
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

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3. P(r) Analysis (GNOM)

dmax	57.1 Å
rg_real	18.56 Å
rg_real_error	0.23 Å
i0_real	1.4160e+07
i0_real_error	1.6980e+05
rg_reciprocal	18.58 Å
i0_reciprocal	14160000.0000
total_estimate	0.9005
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	24.3 Å
skewness	0.065
kurtosis	-0.486
angular_range	— – 0.4250 Å⁻¹
current_alpha	0.0000
highest_alpha	2253000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.978

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Uracil-DNA glycosylase
formula_weight	27492.3 kDa
ec_number	3.2.2.27
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2161

MAHHHHHHTPTLESQFDALPPDWRAILEPFVASDAYAPLCRFVDGERAAGKAIYPADVFRALRLTHPDDVKVVILGQDPYHGEDRGIPQAHGLAFSVPPGVRPPPSLRNIFKEISADFGYEAPRHGCLDTWASQGVLLLNTVLTVERSSAASHAKRGWEKCTDTLIHELATRHRHLVFMLWGAHAQAKRALFDPREHCVLEAPHPSPLSAHRGFLGCRHFALANDYLVKHGRAPIDWRLPDAAETL

Source

organism	Burkholderia thailandensis E264
ncbi_taxonomy_id	271848
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	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	8

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	238

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6. Citations (1)

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length_a	32.629 Å
length_b	63.006 Å
length_c	126.224 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.700 Å
resolution_low	34.990 Å
r_factor	0.1648
r_work	0.1632
r_free	0.1965

fit	/app/data/saxs_computation/py/9pyv/9pyv.fit
pddf	/app/data/pr_computation/py/9pyv/9pyv.pr.out
profile	/app/data/saxs_computation/py/9pyv/9pyv.dat

Crystal structure of Uracil-DNA glycosylase from Burkholderia thailandensis

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