← Back to search

9yzm

;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CTAATTAGGC and loaded with Even-skipped homeodomain ;

Method: X-RAY DIFFRACTION D_max: 99.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9yzm
deposition_date	2025-10-30
last_revision	2026-02-18
title	;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CTAATTAGGC and loaded with Even-skipped homeodomain ;
keywords	Protein-DNA complex, DNA Binding protein, Transcription factor; 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	28.92 Å
rg_electron	27.90 Å
i0	72166100.00
molecular_weight	53644.0 kDa
excluded_volume	61374 Å³
envelope_volume	84677 Å³
shell_volume	27281 Å³
envelope_diameter	104.4 Å
shell_rg	32.53 Å
envelope_rg	28.31 Å
shape_rg	27.84 Å
total_rg	28.42 Å
total_atoms	3707
n_residues	387
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	99.7 Å
rg_real	29.17 Å
rg_real_error	0.83 Å
i0_real	7.2170e+07
i0_real_error	9.7150e+05
rg_reciprocal	29.06 Å
i0_reciprocal	72160000.0000
total_estimate	0.6208
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	29.0 Å
skewness	0.592
kurtosis	-0.106
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	6036000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.716; Smooth: 0.839

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	DNA (31-MER)
formula_weight	9472.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	A
atom_count	3733

CCTGTGACAAATTGCCCTCAGCTAATTAGGC

Entity 2 polymer

description	DNA (31-MER)
formula_weight	9592.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

GGCCTAATTAGCTGAGGGCAATTTGTCACAG

Entity 3 polymer

description	Replication initiation protein
formula_weight	30749.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MRGSHHHHHHGSMAETAVINHKKRKNSPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQIRKSDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDEKGYESFPWFIKPAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDITSMTTG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	Segmentation protein even-skipped
formula_weight	7853.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,E

GTGSVRRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR

Source

organism	Drosophila melanogaster
common_name	fruit fly
ncbi_taxonomy_id	7227
host_organism	Escherichia coli BL21(DE3)

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

▶

6. Citations (2)

▶

length_a	73.781 Å
length_b	125.194 Å
length_c	131.227 Å
angle_alpha	90.00 °
angle_beta	92.26 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.070 Å
resolution_low	44.480 Å
r_factor	0.2604
r_work	0.2594
r_free	0.2691

fit	/app/data/saxs_computation/yz/9yzm/9yzm.fit
pddf	/app/data/pr_computation/yz/9yzm/9yzm.pr.out
profile	/app/data/saxs_computation/yz/9yzm/9yzm.dat

;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CTAATTAGGC and loaded with Even-skipped homeodomain ;

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 (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)