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9yzu

;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence ATGAGTCATA and loaded with mutated Bzip region of GCN4 transcription factor ;

Method: X-RAY DIFFRACTION D_max: 102.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yzu
deposition_date	2025-10-30
last_revision	2026-02-18
title	;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence ATGAGTCATA and loaded with mutated Bzip region of GCN4 transcription factor ;
keywords	Protein-DNA complex, DNA Binding protein, Transcription factor, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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	29.70 Å
rg_electron	29.01 Å
i0	63985600.00
molecular_weight	49673.0 kDa
excluded_volume	56456 Å³
envelope_volume	79129 Å³
shell_volume	25089 Å³
envelope_diameter	106.5 Å
shell_rg	32.82 Å
envelope_rg	29.40 Å
shape_rg	28.94 Å
total_rg	29.50 Å
total_atoms	3421
n_residues	340
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	102.4 Å
rg_real	30.05 Å
rg_real_error	1.26 Å
i0_real	6.3990e+07
i0_real_error	1.0890e+06
rg_reciprocal	29.90 Å
i0_reciprocal	63980000.0000
total_estimate	0.8144
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.0 Å
skewness	0.582
kurtosis	-0.253
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	4663000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.741; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.627; Smooth: 0.744

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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	9496.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	A
atom_count	3445

CCTGTGACAAATTGCCCTCAGATGAGTCATA

Entity 2 polymer

description	DNA (31-MER)
formula_weight	9567.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

GTATGACTCATCTGAGGGCAATTTGTCACAG

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	General control transcription factor GCN4
formula_weight	3422.1 kDa
src_method	syn
entity_count	3

Polymer

type	polypeptide(L)
strand_id	F,D,E

DPAALKRARNTEAARRSRARKLQRMKKQC

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	152.282 Å
length_b	127.186 Å
length_c	72.976 Å
angle_alpha	90.00 °
angle_beta	117.60 °
angle_gamma	90.00 °
z_pdb	12

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.050 Å
resolution_low	63.710 Å
r_factor	0.2268
r_work	0.2247
r_free	0.2457

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

;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence ATGAGTCATA and loaded with mutated Bzip region of GCN4 transcription factor ;

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

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)