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9w3w

Structure of Csm6 from Actinomyces procaprae in complex with cyclic penta-adenylate

Method: ELECTRON MICROSCOPY D_max: 157.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w3w
deposition_date	2025-07-30
title	Structure of Csm6 from Actinomyces procaprae in complex with cyclic penta-adenylate
keywords	;Csm6, Ancillary Nuclease, Allosteric activation, Cyclic Oligoadenylate, Type III CRISPR, IMMUNE SYSTEM/RNA, IMMUNE SYSTEM-RNA complex ;; IMMUNE SYSTEM/RNA
method	ELECTRON MICROSCOPY

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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	49.59 Å
rg_electron	48.79 Å
i0	1873850000.00
molecular_weight	342360.0 kDa
excluded_volume	421630 Å³
envelope_volume	655010 Å³
shell_volume	107920 Å³
envelope_diameter	166.8 Å
shell_rg	55.87 Å
envelope_rg	47.64 Å
shape_rg	48.84 Å
total_rg	48.88 Å
total_atoms	24048
n_residues	3152
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	157.9 Å
rg_real	49.28 Å
rg_real_error	1.02 Å
i0_real	1.8740e+09
i0_real_error	3.5760e+07
rg_reciprocal	49.58 Å
i0_reciprocal	1875000000.0000
total_estimate	0.8610
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.2 Å
skewness	0.217
kurtosis	-0.251
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0001
highest_alpha	243100000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.781

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	;RNA (5'-R(PAPAPAPAP*A)-3') ;
formula_weight	1601.1 kDa
src_method	syn
entity_count	4

Polymer

type	polyribonucleotide
strand_id	1,2,3,4
atom_count	24048

AAAAA

Entity 2 polymer

description	Csm6
formula_weight	85470.3 kDa
src_method	man
entity_count	4

Polymer

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

MTVLVHIVGEGDLGSDILKLKGEQRKQARHAGVTALRTAAVGGTASTPAEAVGLLLDGAASRDHKSRFARTPLALELGAIQAECRSGQVHVLLLGSNSGDGATADIAEALAALLACDEVRAVLHEQYGLEVTAELRADGNLNEQVGRGDLSSWVESAYGTAADRPVVVSMIGGATMMCLSAMGVVDQLGYDWRLAVAGSPDDDAARLVRRGHHGDAPFYWLRALGYLEQAAAWAQEHDREELIDGEHSRLQGDIDAVFGSAGRDDVSSSVTDEQLASLVAVEMARADNGAGLAVRAWVEKHYEALLAEENADRGQDDQISSVFKRLPGKELGKVLGMVRDEQLDQHSASAAWLLKTGDRLRPVGNRAVADAAAPTASELATIKNVPELWRRVPSWMHWPGQGRVLYICGIGAGYRPPSVIERVMEAGPGQELKRAVPGGMLEGGGVGEVDFLLLHSADPGSKRTAVKTCASVLLTTPKDGMIASGVDIIDYGGVSRDQFLAVEETSRKVAGIVREVLETKRPSAVAVVGLGQKGAVIGALEAAQAWCAGHAVPLFVETSVQPGQNIKQPGMQFHRIALHNDAEAALRAAAAASLSSLNLLSAVRVLSAGDRDMDVQAQECDKLREEYLEAVNTKDPDAYAGVLLSVMETIHKLCQEAEGDVDPRLVVVVAEAVNFPRRGKKVAETLFRERYAWQGKENGYSAEWSEVDACGRGDLLRLLYEVRNEVRLTHGDSSVDEAVRAVMRNRFIRISDDFGYEGLLKRAIASVKGGAENLGIDVDDSWAERFQALRGWAEGRS

Source

organism	Actinomyces procaprae
ncbi_taxonomy_id	2560010
host_organism	Escherichia coli

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.67 Å
resolution_method	—
num_particles	143783

fit	/app/data/saxs_computation/w3/9w3w/9w3w.fit
pddf	/app/data/pr_computation/w3/9w3w/9w3w.pr.out
profile	/app/data/saxs_computation/w3/9w3w/9w3w.dat

Structure of Csm6 from Actinomyces procaprae in complex with cyclic penta-adenylate

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)