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9yzr

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

Method: X-RAY DIFFRACTION D_max: 100.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yzr
deposition_date	2025-10-30
last_revision	2026-02-18
title	;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TAATTAGGCCG and loaded with ultrabithorax homeodomain ;
keywords	Protein-DNA complex, DNA Binding protein, Transcription factor; 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	28.31 Å
rg_electron	27.28 Å
i0	65128300.00
molecular_weight	49240.0 kDa
excluded_volume	55505 Å³
envelope_volume	81732 Å³
shell_volume	26859 Å³
envelope_diameter	103.1 Å
shell_rg	32.01 Å
envelope_rg	27.51 Å
shape_rg	27.17 Å
total_rg	27.95 Å
total_atoms	3397
n_residues	360
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	100.5 Å
rg_real	28.65 Å
rg_real_error	0.87 Å
i0_real	6.5130e+07
i0_real_error	8.7340e+05
rg_reciprocal	28.55 Å
i0_reciprocal	65120000.0000
total_estimate	0.8328
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	30.5 Å
skewness	0.631
kurtosis	0.094
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	5034000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.736; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.746; Smooth: 0.867

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4. Crystallography & Experiment

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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	3409

CCTGTGACAAATTGCCCTCATAATTAGGCCG

Entity 2 polymer

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

Polymer

type	polydeoxyribonucleotide
strand_id	B

GCGGCCTAATTATGAGGGCAATTTGTCACAG

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	Homeotic protein ultrabithorax
formula_weight	7911.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,E

GTRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI

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	1

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6. Citations (2)

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length_a	76.032 Å
length_b	124.855 Å
length_c	139.093 Å
angle_alpha	90.00 °
angle_beta	91.85 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.390 Å
resolution_low	45.290 Å
r_factor	0.2684
r_work	0.2652
r_free	0.2976

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

;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TAATTAGGCCG 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

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)