← Back to search

9q7v

One of a series of engineered variants of I-OnuI meganuclease targeting altered DNA target sequence

Method: X-RAY DIFFRACTION D_max: 89.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9q7v
deposition_date	2025-08-25
last_revision	2025-09-10
title	One of a series of engineered variants of I-OnuI meganuclease targeting altered DNA target sequence
keywords	meganuclease, structure prediction, protein engineering, DNA BINDING PROTEIN-DNA complex, DNA BINDING PROTEIN; DNA BINDING PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	24.83 Å
rg_electron	23.82 Å
i0	54654800.00
molecular_weight	48713.0 kDa
excluded_volume	57049 Å³
envelope_volume	69382 Å³
shell_volume	25244 Å³
envelope_diameter	94.9 Å
shell_rg	30.27 Å
envelope_rg	24.19 Å
shape_rg	23.77 Å
total_rg	24.58 Å
total_atoms	3430
n_residues	345
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

▼

3. P(r) Analysis (GNOM)

dmax	89.4 Å
rg_real	25.05 Å
rg_real_error	0.83 Å
i0_real	5.4650e+07
i0_real_error	8.2020e+05
rg_reciprocal	25.00 Å
i0_reciprocal	54650000.0000
total_estimate	0.7376
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	25.5 Å
skewness	0.599
kurtosis	-0.028
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	7653000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.623; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.719; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	eI-OnuI_P456_CCT
formula_weight	34482.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3532

MASSRRESINPWILTGFADAEGSFLLRIRNNNKSSVGYSTELGFQITLHNKDKSILENIQSTWKVGVIANSGDNAVSLKVTRFEDLKVIIDHFEKYPLITQKLGDYKLFKQAFSVMENKEHLKENGIKELVRIKAKLNWGLTDELKKAFPENISKERSLINKNIPNFKWLAGFTSGEGNFFVNLIKSKSKLGVQVQLRFTITQHIKDKNLMNSLITYLGCGYITEKNKSEFSWLDFSVTKFSDINDKIIPVFQENTLIGVKLEDFEDWCKVAKLIEEKKHLTESGLDEIKKIKLNMNKGR

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 2 polymer

description	DNA (26-MER)
formula_weight	7910.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

GGGTTTCCACTTATTCACCTTTTTAG

Entity 3 polymer

description	DNA (26-MER)
formula_weight	8062.3 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

CCTAAAAAGGTGAATAAGTGGAAACC

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	102

▶

6. Citations (1)

▶

length_a	49.007 Å
length_b	63.256 Å
length_c	167.053 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	2.356 Å
resolution_low	28.402 Å
r_factor	0.1924
r_work	0.1871
r_free	0.2450

fit	/app/data/saxs_computation/q7/9q7v/9q7v.fit
pddf	/app/data/pr_computation/q7/9q7v/9q7v.pr.out
profile	/app/data/saxs_computation/q7/9q7v/9q7v.dat

One of a series of engineered variants of I-OnuI meganuclease targeting altered DNA target sequence

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)