5hmC specific restriction endonuclease Escherichia coli APEC O1 PD-T4-3

Method: X-RAY DIFFRACTION D_max: 69.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u7u
deposition_date	2025-03-25
title	5hmC specific restriction endonuclease Escherichia coli APEC O1 PD-T4-3
keywords	Restriction endonuclease, defense system, GIY-YIG, PD-T4-3, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	20.83 Å
rg_electron	20.19 Å
i0	13982300.00
molecular_weight	27962.0 kDa
excluded_volume	34961 Å³
envelope_volume	42705 Å³
shell_volume	18376 Å³
envelope_diameter	71.4 Å
shell_rg	25.57 Å
envelope_rg	20.09 Å
shape_rg	20.18 Å
total_rg	20.99 Å
total_atoms	3910
n_residues	246
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	69.7 Å
rg_real	20.80 Å
rg_real_error	0.52 Å
i0_real	1.3980e+07
i0_real_error	1.9190e+05
rg_reciprocal	20.81 Å
i0_reciprocal	13980000.0000
total_estimate	0.8126
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.2 Å
skewness	0.302
kurtosis	-0.367
angular_range	— – 0.3800 Å⁻¹
current_alpha	0.0000
highest_alpha	3533000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	123.332 Å
length_b	123.332 Å
length_c	82.932 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 64 2 2
int_tables_number	181
crystal_system	—

resolution	2.194 Å
resolution_low	38.655 Å
r_factor	0.2236
r_work	0.2217
r_free	0.2583

description	GIY-YIG domain-containing protein
formula_weight	29530.5 kDa
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	3982

5hmC specific restriction endonuclease Escherichia coli APEC O1 PD-T4-3

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Escherichia coli APEC O1
ncbi_taxonomy_id	405955
host_organism	Escherichia coli BL21(DE3)

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	72

fit	/app/data/saxs_computation/u7/9u7u/9u7u.fit
pddf	/app/data/pr_computation/u7/9u7u/9u7u.pr.out
profile	/app/data/saxs_computation/u7/9u7u/9u7u.dat