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9yzq

;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with Engrailed homeodomain enhanced Green fluorescent protein fusion ;

Method: X-RAY DIFFRACTION D_max: 100.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yzq
deposition_date	2025-10-30
last_revision	2026-02-18
title	;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with Engrailed homeodomain enhanced Green fluorescent protein fusion ;
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	28.01 Å
rg_electron	27.12 Å
i0	60509000.00
molecular_weight	46399.0 kDa
excluded_volume	51831 Å³
envelope_volume	75703 Å³
shell_volume	25747 Å³
envelope_diameter	106.2 Å
shell_rg	30.74 Å
envelope_rg	27.37 Å
shape_rg	26.98 Å
total_rg	27.74 Å
total_atoms	3192
n_residues	334
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	100.8 Å
rg_real	28.40 Å
rg_real_error	1.11 Å
i0_real	6.0510e+07
i0_real_error	1.0110e+06
rg_reciprocal	28.28 Å
i0_reciprocal	60500000.0000
total_estimate	0.6053
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	30.1 Å
skewness	0.690
kurtosis	0.222
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	4132000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.672; Stabil: 1.000; Sysdev: 0.075; Positv: 1.000; Valcen: 0.753; Smooth: 0.869

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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	3198

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	Segmentation polarity homeobox protein engrailed,Green fluorescent protein
formula_weight	36124.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKSTSQFYLNEMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKHHHHHH

Source

organism	Aequorea victoria
common_name	Water jellyfish, Mesonema victoria
ncbi_taxonomy_id	6100
host_organism	Escherichia coli BL21(DE3)

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	74.116 Å
length_b	122.397 Å
length_c	140.438 Å
angle_alpha	90.00 °
angle_beta	90.38 °
angle_gamma	90.00 °
z_pdb	4

space_group	I 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.750 Å
resolution_low	46.920 Å
r_factor	0.2992
r_work	0.2951
r_free	0.3382

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

;Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with Engrailed homeodomain enhanced Green fluorescent protein fusion ;

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 (1)

7. Files & Curves (10)

Files (7)

Curves (3)