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9z4e

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

Method: X-RAY DIFFRACTION D_max: 100.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z4e
deposition_date	2025-11-10
last_revision	2026-02-18
title	;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CATGAGTCAT 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	29.55 Å
rg_electron	29.08 Å
i0	57648200.00
molecular_weight	46026.0 kDa
excluded_volume	51640 Å³
envelope_volume	75826 Å³
shell_volume	24148 Å³
envelope_diameter	106.0 Å
shell_rg	32.45 Å
envelope_rg	29.77 Å
shape_rg	29.01 Å
total_rg	29.50 Å
total_atoms	3166
n_residues	328
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	100.3 Å
rg_real	29.93 Å
rg_real_error	0.91 Å
i0_real	5.7650e+07
i0_real_error	8.6770e+05
rg_reciprocal	29.77 Å
i0_reciprocal	57640000.0000
total_estimate	0.7623
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.0 Å
skewness	0.609
kurtosis	-0.241
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	4394000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.736; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.651; Smooth: 0.046

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	General control transcription factor GCN4
formula_weight	3422.1 kDa
mutation	residues 251-253 (Uniprot numbering) mutated from KQL to KKQC
src_method	syn
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,F,E
atom_count	3172

DPAALKRARNTEAARRSRARKLQRMKKQC

Entity 2 polymer

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

Polymer

type	polydeoxyribonucleotide
strand_id	A

CCTGTGACAAATTGCCCTCAGCATGAGTCAT

Entity 3 polymer

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

Polymer

type	polydeoxyribonucleotide
strand_id	B

GATGACTCATGCTGAGGGCAATTTGTCACAG

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	3

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6. Citations (2)

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length_a	159.036 Å
length_b	115.325 Å
length_c	72.715 Å
angle_alpha	90.00 °
angle_beta	116.50 °
angle_gamma	90.00 °
z_pdb	12

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.630 Å
resolution_low	65.070 Å
r_factor	0.2512
r_work	0.2473
r_free	0.2853

fit	/app/data/saxs_computation/z4/9z4e/9z4e.fit
pddf	/app/data/pr_computation/z4/9z4e/9z4e.pr.out
profile	/app/data/saxs_computation/z4/9z4e/9z4e.dat

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

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)