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9z44

;Isoreticular co-crystal 1 with symmetrical expanded duplex (31mer) containing insert sequence CCCGGCCGGA and loaded with C-clamp domain ;

Method: X-RAY DIFFRACTION D_max: 108.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z44
deposition_date	2025-11-08
last_revision	2026-02-25
title	;Isoreticular co-crystal 1 with symmetrical expanded duplex (31mer) containing insert sequence CCCGGCCGGA and loaded with C-clamp domain ;
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	28.23 Å
rg_electron	27.34 Å
i0	52130900.00
molecular_weight	41153.0 kDa
excluded_volume	44899 Å³
envelope_volume	69325 Å³
shell_volume	23807 Å³
envelope_diameter	113.8 Å
shell_rg	30.66 Å
envelope_rg	27.00 Å
shape_rg	27.18 Å
total_rg	27.95 Å
total_atoms	2821
n_residues	299
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	108.7 Å
rg_real	28.61 Å
rg_real_error	1.08 Å
i0_real	5.2130e+07
i0_real_error	8.5370e+05
rg_reciprocal	28.49 Å
i0_reciprocal	52130000.0000
total_estimate	0.7940
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.0 Å
skewness	0.657
kurtosis	0.302
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	3087000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.601; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.547; Smooth: 0.967

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DNA (31-MER)
formula_weight	9459.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	A
atom_count	2821

GCCGGACCTGTGACAAATTGCCCTCAGCCCG

Entity 2 polymer

description	DNA (31-MER)
formula_weight	9610.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

GCCGGGCTGAGGGCAATTTGTCACAGGTCCG

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	SLC2A4 regulator
formula_weight	4032.8 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

GDAKKCRKVYGMERRDLWCTACRWKKACQRFLD

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6. Citations (2)

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length_a	73.491 Å
length_b	127.653 Å
length_c	141.183 Å
angle_alpha	90.00 °
angle_beta	91.98 °
angle_gamma	90.00 °
z_pdb	4

space_group	I 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	7.200 Å
resolution_low	47.990 Å
r_factor	0.2870
r_work	0.2804
r_free	0.3453

fit	/app/data/saxs_computation/z4/9z44/9z44.fit
pddf	/app/data/pr_computation/z4/9z44/9z44.pr.out
profile	/app/data/saxs_computation/z4/9z44/9z44.dat

;Isoreticular co-crystal 1 with symmetrical expanded duplex (31mer) containing insert sequence CCCGGCCGGA and loaded with C-clamp domain ;

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 (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)