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9u7z

5hmC specific restriction endonuclease Escherichia coli APEC O1 PD-T4-3 in complex with 5-Hydroxymethyl-dCTP

Method: X-RAY DIFFRACTION D_max: 70.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u7z
deposition_date	2025-03-25
title	5hmC specific restriction endonuclease Escherichia coli APEC O1 PD-T4-3 in complex with 5-Hydroxymethyl-dCTP
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	21.21 Å
rg_electron	20.30 Å
i0	14958900.00
molecular_weight	28479.0 kDa
excluded_volume	35375 Å³
envelope_volume	43900 Å³
shell_volume	18698 Å³
envelope_diameter	71.4 Å
shell_rg	25.98 Å
envelope_rg	20.28 Å
shape_rg	20.28 Å
total_rg	21.17 Å
total_atoms	3951
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	70.1 Å
rg_real	21.18 Å
rg_real_error	0.37 Å
i0_real	1.4960e+07
i0_real_error	1.8750e+05
rg_reciprocal	21.19 Å
i0_reciprocal	14960000.0000
total_estimate	0.8950
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	69.0 Å
skewness	0.288
kurtosis	-0.414
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	4583000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

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

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4126

SASGSMDINEFPSGVIEHLGWYVYRLIDPRDGSTFYVGKGKGNRVFAHMRGEVAAVDDDELLNNKLRQLREIRLAGLDVIHVIHRHGMAEEKTAYEVEAALIDAYPGLTNIMNGAGSNEFGAAHIKELIATYQPETITFQHKALMISVNRSSKDIDLYDAVRFSWRVSVDRARKAEIILATVRGIVRGVYIADEWLKSTRENFPEMTSWEADDEFEATQCSRFGFRGRVASPEITQLYIGKKIPDDLRKKGAMSPVRYSPGF

Source

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

Entity 2 non-polymer

description	;[[(2R,3S,5R)-5-[4-azanyl-5-(hydroxymethyl)-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate ;
formula_weight	497.2 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	132

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6. Citations (1)

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length_a	124.728 Å
length_b	124.728 Å
length_c	80.796 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	2.153 Å
resolution_low	49.368 Å
r_factor	0.2325
r_work	0.2304
r_free	0.2730

fit	/app/data/saxs_computation/u7/9u7z/9u7z.fit
pddf	/app/data/pr_computation/u7/9u7z/9u7z.pr.out
profile	/app/data/saxs_computation/u7/9u7z/9u7z.dat

5hmC specific restriction endonuclease Escherichia coli APEC O1 PD-T4-3 in complex with 5-Hydroxymethyl-dCTP

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