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9yup

Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans

Method: X-RAY DIFFRACTION D_max: 149.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yup
deposition_date	2025-10-22
last_revision	2025-10-29
title	Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans
keywords	;PprA, Deinococcus, Deinococcus radiodurans, D. radiodurans, DNA repair, DNA binding protein, Genome reassembly, self-assembly, protein filament ;; DNA BINDING PROTEIN
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	46.48 Å
rg_electron	46.38 Å
i0	239992000.00
molecular_weight	121030.0 kDa
excluded_volume	148980 Å³
envelope_volume	238070 Å³
shell_volume	44491 Å³
envelope_diameter	162.8 Å
shell_rg	48.82 Å
envelope_rg	44.92 Å
shape_rg	46.30 Å
total_rg	46.75 Å
total_atoms	16789
n_residues	1097
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	149.9 Å
rg_real	46.62 Å
rg_real_error	1.61 Å
i0_real	2.4000e+08
i0_real_error	4.8610e+06
rg_reciprocal	46.48 Å
i0_reciprocal	239900000.0000
total_estimate	0.8324
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	44.1 Å
skewness	0.201
kurtosis	-0.806
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	9609000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; Smooth: 0.334

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	DNA repair protein PprA
formula_weight	33602.8 kDa
mutation	D180K, D184K
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	16960

MRSGSHHHHHHRSDITSLYKKAGLENLYFQGQTDGIYAAFDTLMSTAGVDSQIAALAASEADAGTLDAALTQSLQEAQGRWGLGLHHLRHEARLTDDGDIEILTDGRPSARVSEGFGALAQAYAPMQALDERGLSQWAALGEGYRAPGDLPLAQLKVLIEHARDFETDWSAGRGETFQRVWRKGDTLFVEVARPASAEAALSKAAWKVIASIKDRAFQRELMRRSEKDGMLGALLGARHAGAKANLAQLPEAHFTVQAFVQTLSGAAARNAEEYRAALKTAAAALEEYQGVTTRQLSEVLRHGLRES

Source

organism	Deinococcus radiodurans
ncbi_taxonomy_id	1299
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	CITRATE ANION
formula_weight	189.1 kDa
src_method	syn
entity_count	3

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	171

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6. Citations (1)

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length_a	49.679 Å
length_b	123.221 Å
length_c	139.288 Å
angle_alpha	90.00 °
angle_beta	93.69 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.070 Å
resolution_low	41.650 Å
r_factor	0.2119
r_work	0.2107
r_free	0.2361

fit	/app/data/saxs_computation/yu/9yup/9yup.fit
pddf	/app/data/pr_computation/yu/9yup/9yup.pr.out
profile	/app/data/saxs_computation/yu/9yup/9yup.dat

Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans

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