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9w2k

;Structural basis of substrate promiscuity in the archaeal RNA-splicing endonuclease from Candidatus Micrarchaeum acidiphilum (ARMAN-2) ;

Method: X-RAY DIFFRACTION D_max: 104.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w2k
deposition_date	2025-07-28
last_revision	2025-09-10
title	;Structural basis of substrate promiscuity in the archaeal RNA-splicing endonuclease from Candidatus Micrarchaeum acidiphilum (ARMAN-2) ;
keywords	Archaea, tRNA, Intron, Novel catalytic reaction, SPLICING, SPLICING-RNA complex; SPLICING/RNA
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	30.07 Å
rg_electron	29.59 Å
i0	160514000.00
molecular_weight	97647.0 kDa
excluded_volume	120930 Å³
envelope_volume	147490 Å³
shell_volume	41042 Å³
envelope_diameter	107.9 Å
shell_rg	37.09 Å
envelope_rg	29.95 Å
shape_rg	29.54 Å
total_rg	30.37 Å
total_atoms	6860
n_residues	795
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	104.5 Å
rg_real	30.08 Å
rg_real_error	0.97 Å
i0_real	1.6050e+08
i0_real_error	2.6370e+06
rg_reciprocal	30.07 Å
i0_reciprocal	160500000.0000
total_estimate	0.8543
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.5 Å
skewness	0.446
kurtosis	0.032
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	37280000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.715; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.964

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	tRNA intron endonuclease
formula_weight	45882.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7209

MTLLLNINTKAKRISVSDQSTIDILRNGYFGEYRAGKLMLEVEEGLYLVDVRKAACTDENSKPVSFNDIAGVFIKRKKLMARYFTFKDWRDRGLIIKSPGLRFGEEEHVQAKRYPSSAINLKKYSVTGIFFPDDMVTVIDDDESGKDLYENFWLGQYGTYKVSEHGNLNKLDIYETLFLIDMGVISIKNFTRAQIVNIASARRTDIMKLYDVYKDWRTKGYVVKTGFKFGTNFRIYFPGAKPIKENNEWIHSKHVLHVFPRDSKLIISEWARAIRVAHSVRKTFILAIPGKTRKKKLAIDFELYHRRGGDIEIPGKNSPRFGMLSLSENERIGGSELSAIINEAKSRKLELVIAIADSETSVTYYKVRRVDLPKSEYEYYEIDWMQPLEHHHHHH

Source

organism	Candidatus Micrarchaeum acidiphilum ARMAN-2
ncbi_taxonomy_id	425595
host_organism	Escherichia

Entity 2 polymer

description	;DNA/RNA (5'-R(PAPCPCPGPAPCPCPA)-D(PU)-R(PAPGPCP*U)-3') ;
formula_weight	4084.5 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	I

ACCGACCAUAGCU

Entity 3 polymer

description	;RNA (5'-R(PAPGPCPGPGPUPCPA)-3') ;
formula_weight	2565.6 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	F

AGCGGUCA

Entity 4 polymer

description	;RNA (5'-R(APGPGPU)-3') ;
formula_weight	1280.8 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	H

AGGU

Entity 5 non-polymer

description	ACETIC ACID
formula_weight	60.1 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	;ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE ;
formula_weight	409.2 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	349

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6. Citations (1)

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length_a	53.514 Å
length_b	65.648 Å
length_c	71.802 Å
angle_alpha	114.46 °
angle_beta	111.89 °
angle_gamma	90.01 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.798 Å
resolution_low	33.529 Å
r_factor	—
r_work	0.1853
r_free	0.2310

fit	/app/data/saxs_computation/w2/9w2k/9w2k.fit
pddf	/app/data/pr_computation/w2/9w2k/9w2k.pr.out
profile	/app/data/saxs_computation/w2/9w2k/9w2k.dat

;Structural basis of substrate promiscuity in the archaeal RNA-splicing endonuclease from Candidatus Micrarchaeum acidiphilum (ARMAN-2) ;

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)