Crystal structure of the Clostridiodes difficile CspA homodimer

Method: X-RAY DIFFRACTION D_max: 172.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pr9
deposition_date	2025-07-23
title	Crystal structure of the Clostridiodes difficile CspA homodimer
keywords	Pseudoproteases, homodimer, signaling proteins, SIGNALING PROTEIN; SIGNALING 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	49.36 Å
rg_electron	49.62 Å
i0	705079000.00
molecular_weight	222650.0 kDa
excluded_volume	279360 Å³
envelope_volume	379000 Å³
shell_volume	65469 Å³
envelope_diameter	176.0 Å
shell_rg	51.14 Å
envelope_rg	48.59 Å
shape_rg	49.62 Å
total_rg	49.67 Å
total_atoms	15720
n_residues	2076
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	172.3 Å
rg_real	49.86 Å
rg_real_error	2.17 Å
i0_real	7.0510e+08
i0_real_error	1.6140e+07
rg_reciprocal	49.37 Å
i0_reciprocal	704600000.0000
total_estimate	0.8160
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	43.1 Å
skewness	0.467
kurtosis	-0.547
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	59540000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.670; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.831; Smooth: 0.763

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

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6. Citations (1)

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length_a	125.980 Å
length_b	131.930 Å
length_c	155.327 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	3.260 Å
resolution_low	100.550 Å
r_factor	0.2810
r_work	0.2789
r_free	0.3215

description	Germination-specific protease
formula_weight	61329.4 kDa
src_method	man
entity_count	4

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	15720

Crystal structure of the Clostridiodes difficile CspA homodimer

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 (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Clostridia
ncbi_taxonomy_id	186801
host_organism	Escherichia

fit	/app/data/saxs_computation/pr/9pr9/9pr9.fit
pddf	/app/data/pr_computation/pr/9pr9/9pr9.pr.out
profile	/app/data/saxs_computation/pr/9pr9/9pr9.dat