← Back to search

9yzp

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

Method: X-RAY DIFFRACTION D_max: 100.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9yzp
deposition_date	2025-10-30
last_revision	2026-02-18
title	;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with ultrabithorax 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	28.21 Å
rg_electron	27.23 Å
i0	58923700.00
molecular_weight	46108.0 kDa
excluded_volume	51641 Å³
envelope_volume	74730 Å³
shell_volume	25344 Å³
envelope_diameter	104.3 Å
shell_rg	30.86 Å
envelope_rg	27.69 Å
shape_rg	27.11 Å
total_rg	27.82 Å
total_atoms	3171
n_residues	334
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	100.8 Å
rg_real	28.63 Å
rg_real_error	1.03 Å
i0_real	5.8920e+07
i0_real_error	9.0380e+05
rg_reciprocal	28.50 Å
i0_reciprocal	58920000.0000
total_estimate	0.6393
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	30.6 Å
skewness	0.689
kurtosis	0.182
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	3942000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.691; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.694; Smooth: 0.811

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	Homeotic protein ultrabithorax
formula_weight	7911.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D
atom_count	3177

GTRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI

Source

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

Entity 2 polymer

description	DNA (31-MER)
formula_weight	9528.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	A

CCTGTGACAAATTGCCCTGCTTGATGAGCAG

Entity 3 polymer

description	DNA (31-MER)
formula_weight	9537.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

GCTGCTCATCAAGCAGGGCAATTTGTCACAG

Entity 4 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 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

▶

6. Citations (2)

▶

length_a	73.917 Å
length_b	126.606 Å
length_c	137.886 Å
angle_alpha	90.00 °
angle_beta	90.92 °
angle_gamma	90.00 °
z_pdb	4

space_group	I 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.670 Å
resolution_low	47.160 Å
r_factor	0.2745
r_work	0.2720
r_free	0.2949

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

;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with ultrabithorax 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

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)