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9u8d

5hmC specific restriction endonuclease Escherichia coli O157:H7 PD-T4-3 in complex with 5-Hydroxymethyl-dCTP

Method: X-RAY DIFFRACTION D_max: 100.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u8d
deposition_date	2025-03-26
title	5hmC specific restriction endonuclease Escherichia coli O157:H7 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	31.86 Å
rg_electron	31.28 Å
i0	386194000.00
molecular_weight	105110.0 kDa
excluded_volume	101510 Å³
envelope_volume	183240 Å³
shell_volume	48284 Å³
envelope_diameter	99.9 Å
shell_rg	38.99 Å
envelope_rg	30.81 Å
shape_rg	31.29 Å
total_rg	31.73 Å
total_atoms	8000
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	100.3 Å
rg_real	31.68 Å
rg_real_error	0.88 Å
i0_real	3.8620e+08
i0_real_error	6.1010e+06
rg_reciprocal	31.76 Å
i0_reciprocal	386200000.0000
total_estimate	0.8949
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	40.1 Å
skewness	0.183
kurtosis	-0.421
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	36090000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.939

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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	29482.4 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8002

SASGSMDITEFPSGVIEHLGWYVYRLIDPRDGSTFYVGKGKGNRVFAHMRGEVAAADDDDLLSNKLKQIREIRLAGLEVIHVIHRHGMTDEKTAYEVEAALIDAYPGLTNIMNGAGSNEFGAAHVKELIATYQPETITFHHKALMISVNRSAKDSELYDAVRFSWRINVSRASKAEVILATVRGIVRGVFIADKWLKSTREHFPTMKYWDEDPDFEATQSSRYGFEGREAPPEIANLYLGKKIPDELRKKGAMSPVRYSPNF

Source

organism	Escherichia coli O157:H7
ncbi_taxonomy_id	83334
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	2

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6. Citations (1)

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length_a	103.621 Å
length_b	103.621 Å
length_c	126.360 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	3.002 Å
resolution_low	47.937 Å
r_factor	0.2288
r_work	0.2265
r_free	0.2687

fit	/app/data/saxs_computation/u8/9u8d/9u8d.fit
pddf	/app/data/pr_computation/u8/9u8d/9u8d.pr.out
profile	/app/data/saxs_computation/u8/9u8d/9u8d.dat

5hmC specific restriction endonuclease Escherichia coli O157:H7 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