5hmC specific restriction endonuclease Escherichia coli E. coli O157:H7 PD-T4-3

Method: X-RAY DIFFRACTION D_max: 97.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u75
deposition_date	2025-03-24
title	5hmC specific restriction endonuclease Escherichia coli E. coli O157:H7 PD-T4-3
keywords	Restriction endonuclease, defense system, GIY-YIG, PD-Y4-3, 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	31.85 Å
rg_electron	31.20 Å
i0	196413000.00
molecular_weight	112520.0 kDa
excluded_volume	141110 Å³
envelope_volume	182210 Å³
shell_volume	48152 Å³
envelope_diameter	99.9 Å
shell_rg	38.91 Å
envelope_rg	30.71 Å
shape_rg	31.20 Å
total_rg	31.81 Å
total_atoms	7956
n_residues	991
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	97.8 Å
rg_real	31.67 Å
rg_real_error	0.66 Å
i0_real	1.9640e+08
i0_real_error	2.9980e+06
rg_reciprocal	31.75 Å
i0_reciprocal	196400000.0000
total_estimate	0.8842
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	41.1 Å
skewness	0.184
kurtosis	-0.413
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	37920000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.728

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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	103.629 Å
length_b	103.629 Å
length_c	125.830 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 41
int_tables_number	76
crystal_system	—

resolution	2.803 Å
resolution_low	47.911 Å
r_factor	0.2284
r_work	0.2264
r_free	0.2858

description	GIY-YIG domain-containing protein
formula_weight	29482.4 kDa
src_method	man
entity_count	4

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	7960

5hmC specific restriction endonuclease Escherichia coli E. coli O157:H7 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 O157:H7
ncbi_taxonomy_id	83334
host_organism	Escherichia coli BL21(DE3)

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	4

fit	/app/data/saxs_computation/u7/9u75/9u75.fit
pddf	/app/data/pr_computation/u7/9u75/9u75.pr.out
profile	/app/data/saxs_computation/u7/9u75/9u75.dat