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9z08

Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing separate insert strand with sequence GACGGTAATT

Method: X-RAY DIFFRACTION D_max: 104.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z08
deposition_date	2025-10-31
last_revision	2026-03-18
title	Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing separate insert strand with sequence GACGGTAATT
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	27.97 Å
rg_electron	26.77 Å
i0	50753800.00
molecular_weight	42912.0 kDa
excluded_volume	48138 Å³
envelope_volume	69497 Å³
shell_volume	23829 Å³
envelope_diameter	107.0 Å
shell_rg	30.56 Å
envelope_rg	27.69 Å
shape_rg	26.61 Å
total_rg	27.44 Å
total_atoms	2946
n_residues	275
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	104.5 Å
rg_real	28.40 Å
rg_real_error	0.96 Å
i0_real	5.0750e+07
i0_real_error	8.1890e+05
rg_reciprocal	28.27 Å
i0_reciprocal	50750000.0000
total_estimate	0.7967
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	29.3 Å
skewness	0.683
kurtosis	0.158
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	3489000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.620; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.573; Smooth: 0.917

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	;DNA (5'-D(PAPCPCPTPGPTPGPAPCPAPAPAPTPTGPCPCPCPTPCP*A)-3') ;
formula_weight	6367.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	A
atom_count	2980

ACCTGTGACAAATTGCCCTCA

Entity 2 polymer

description	;DNA (5'-D(PTPCPTPGPAPGPGPGPCPAPAPTPTPTPGPTPCPAPCPAP*G)-3') ;
formula_weight	6478.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

TCTGAGGGCAATTTGTCACAG

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	;DNA (5'-D(PGPAPCPGPGPTPAPAPTPT)-3') ;
formula_weight	3084.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E

GACGGTAATT

Entity 5 polymer

description	;DNA (5'-D(PGPTPAPAPTPTPAPCPCPG)-3') ;
formula_weight	3044.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	F

GTAATTACCG

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

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6. Citations (2)

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length_a	75.045 Å
length_b	133.505 Å
length_c	135.653 Å
angle_alpha	90.00 °
angle_beta	96.08 °
angle_gamma	90.00 °
z_pdb	4

space_group	I 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	4.220 Å
resolution_low	37.310 Å
r_factor	0.2413
r_work	0.2398
r_free	0.2537

fit	/app/data/saxs_computation/z0/9z08/9z08.fit
pddf	/app/data/pr_computation/z0/9z08/9z08.pr.out
profile	/app/data/saxs_computation/z0/9z08/9z08.dat

Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing separate insert strand with sequence GACGGTAATT

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 (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)