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9yzl

;Isoreticular co-crystal of Replication Initiator Protein REPE54 and asymmetrical expanded duplex (31mer) containing the cognate REPE54 sequence, and additional T-A rich sequence with 5' terminal phosphates. Two copies of Even-skipped homeodomain loaded post-crystallization ;

Method: X-RAY DIFFRACTION D_max: 99.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yzl
deposition_date	2025-10-30
last_revision	2026-02-18
title	;Isoreticular co-crystal of Replication Initiator Protein REPE54 and asymmetrical expanded duplex (31mer) containing the cognate REPE54 sequence, and additional T-A rich sequence with 5' terminal phosphates. Two copies of Even-skipped homeodomain loaded post-crystallization ;
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	27.83 Å
rg_electron	26.64 Å
i0	64212500.00
molecular_weight	50406.0 kDa
excluded_volume	57606 Å³
envelope_volume	77010 Å³
shell_volume	25998 Å³
envelope_diameter	103.6 Å
shell_rg	31.07 Å
envelope_rg	27.63 Å
shape_rg	26.52 Å
total_rg	27.30 Å
total_atoms	3476
n_residues	342
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	99.4 Å
rg_real	28.22 Å
rg_real_error	1.08 Å
i0_real	6.4210e+07
i0_real_error	1.0900e+06
rg_reciprocal	28.10 Å
i0_reciprocal	64210000.0000
total_estimate	0.8187
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.6 Å
skewness	0.679
kurtosis	0.135
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	4524000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.684; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.738; Smooth: 0.850

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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	9472.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	A
atom_count	3490

CCTGTGACAAATTGCCCTCAGCTAATTAGGC

Entity 2 polymer

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

Polymer

type	polydeoxyribonucleotide
strand_id	B

GGCCTAATTAGCTGAGGGCAATTTGTCACAG

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 protein even-skipped
formula_weight	7853.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,D

GTGSVRRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR

Source

organism	Drosophila melanogaster
common_name	fruit fly
ncbi_taxonomy_id	7227
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	73.365 Å
length_b	120.285 Å
length_c	134.401 Å
angle_alpha	90.00 °
angle_beta	91.47 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.020 Å
resolution_low	44.810 Å
r_factor	0.2836
r_work	0.2825
r_free	0.2942

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

;Isoreticular co-crystal of Replication Initiator Protein REPE54 and asymmetrical expanded duplex (31mer) containing the cognate REPE54 sequence, and additional T-A rich sequence with 5' terminal phosphates. Two copies of Even-skipped homeodomain loaded post-crystallization ;

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)