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9yza

;Isoreticular co-crystal 1 of protein variant Replication Initiator Protein REPE54 (L53G, Q54G, E55G) with symmetrical expanded duplex (31mer) containing insert sequence CCCGGCCGGA ;

Method: X-RAY DIFFRACTION D_max: 103.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yza
deposition_date	2025-10-30
last_revision	2026-02-18
title	;Isoreticular co-crystal 1 of protein variant Replication Initiator Protein REPE54 (L53G, Q54G, E55G) with symmetrical expanded duplex (31mer) containing insert sequence CCCGGCCGGA ;
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	27.03 Å
rg_electron	25.35 Å
i0	51846300.00
molecular_weight	43894.0 kDa
excluded_volume	49489 Å³
envelope_volume	65521 Å³
shell_volume	23383 Å³
envelope_diameter	106.7 Å
shell_rg	29.94 Å
envelope_rg	26.05 Å
shape_rg	25.19 Å
total_rg	26.10 Å
total_atoms	3014
n_residues	279
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	103.3 Å
rg_real	27.36 Å
rg_real_error	1.27 Å
i0_real	5.1850e+07
i0_real_error	8.1200e+05
rg_reciprocal	27.26 Å
i0_reciprocal	51840000.0000
total_estimate	0.7878
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.8 Å
skewness	0.675
kurtosis	0.321
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	3571000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.601; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.475; Smooth: 0.959

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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	3044

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

CCGGGCTGAGGGCAATTTGTCACAGGTCCGG

Entity 3 polymer

description	Replication initiation protein
formula_weight	30549.8 kDa
mutation	L53G, Q54G, E55G
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MRGSHHHHHHGSMAETAVINHKKRKNSPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQIRKSDGTGGGHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDEKGYESFPWFIKPAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDITSMTTG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 4 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	74.346 Å
length_b	124.350 Å
length_c	137.538 Å
angle_alpha	90.00 °
angle_beta	90.30 °
angle_gamma	90.00 °
z_pdb	4

space_group	I 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.050 Å
resolution_low	46.670 Å
r_factor	0.2972
r_work	0.2959
r_free	0.3090

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

;Isoreticular co-crystal 1 of protein variant Replication Initiator Protein REPE54 (L53G, Q54G, E55G) with symmetrical expanded duplex (31mer) containing insert sequence CCCGGCCGGA ;

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)