SAXSdb — 9x25

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1. Structure Basics

entry_id	9x25
deposition_date	2025-10-03
last_revision	2025-12-10
title	Target analog-bound type III-B Cmr complex of Archaeoglobus fulgidus
keywords	Type III-B CRISPR-Cas effector, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA-DNA complex; RNA BINDING PROTEIN/RNA/DNA
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	48.49 Å
rg_electron	48.69 Å
i0	1424790000.00
molecular_weight	308500.0 kDa
excluded_volume	383060 Å³
envelope_volume	536280 Å³
shell_volume	91277 Å³
envelope_diameter	163.7 Å
shell_rg	53.43 Å
envelope_rg	47.83 Å
shape_rg	48.73 Å
total_rg	48.70 Å
total_atoms	21810
n_residues	2992
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	164.4 Å
rg_real	48.56 Å
rg_real_error	1.42 Å
i0_real	1.4250e+09
i0_real_error	2.7970e+07
rg_reciprocal	48.49 Å
i0_reciprocal	1425000000.0000
total_estimate	0.8710
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	51.4 Å
skewness	0.362
kurtosis	-0.501
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	395700000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.854

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	crRNA
formula_weight	12604.5 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	A
atom_count	21810

AUUGAAAGUUGUAGUAUGCGGUCCUUGCGGCUGAGAGCA

Entity 2 polymer

description	GGDEF domain-containing protein
formula_weight	117383.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MGSSHHHHHHSSGLVPRGSHMGQYFRVSGKYRGRENLPREVNKMADNEFWLNKIRAFFHDPPDKSFELKTHERRASFILGELKPSKSLKRIIKNADIQASSLQRVDLEKSIHKKELKSTFDRIHNTEKYEYIGQPIIRHPVTGEIKEYGTILANLPQTQREVYDVDDEGKEDYEEQFQEILSRILKIEKKVFDDFKNRYSDPKDLYISLWAFYAEKLKEALEEEFSASFAEEFVNLPAYTLSPDHTLFDHADATSAIFGAEIDGKKPVLVLFKISPVQKFIADARKEKDLWAASHMLSTLTFKAISFIADKFGPDVVIYPHLRGNPFFHAWLHSKKIWEFSDSHSLKIASVPNKFLALVGVSDEKELNNLREGIRNEIESFLADLFDKLWNEVIVGALEHSDALKHLGDKKEIHKEILLKRFTLTLSSLKIHDVDVSGSKEEAYEKVKDFVRSLGLPNAIESKYLQWLDMLGSVEASNNRPTKYDLYSLYYEILTVLNAIESTHFDKPAEPAGYKCTLCGEHLAIGGESREMMENVWGKIHKRWPSHLRSNERLCAVCAVKRFYPKFIETLDIFEGVGKVVPDIESVSEVAMCRRTKHGITWKEVYDYLRGLKNVDDEKLLGKLENLKHSVQTLINNVKSELKSRKVYPEEFLEGLNRNFSNEILYSERLRDFNTLLDTLGFDAAKLGLDDVKNYETMISELRERLSEVYKMLGEPPKYYAILMMDGDEMGKLLSGEKLKTAEHYLHSAILERVSDALRVKAKTVRRLITPAAHSSISRALKNFSVNHVPDVVRKGNGTLIYSGGDDVLVLLPVDTAFDVATELAMTFSTSWNGWEMLPGNKLSAGLLIVHYKHPLYDALEKTRELLQKAKKLGRNAIAVGLLKRSGSYYESVVNFETLEDAKAVANLLVKEQVSPRIIYELLNFADVISKEFLHQLVKYEAVRHSIDKNLAEEFQSVFARGHQGVRVELEGNDEEINKYISDGANLETFLDKYEKAVDVIRKQVRGFLNLVKILYESIRGGAK

Source

organism	Archaeoglobus fulgidus DSM 4304
ncbi_taxonomy_id	224325
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	Type III-B CRISPR module-associated protein Cmr3
formula_weight	39043.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MILVMKPYDSLLFREPRPFDVNNHVARTILPLPQTLAGAVRSAIYVKYGSKVKDLIGFGKEEPEFEILGHFFYRYDGKFELLVESPHDVTQNLGLVKPHRIDKLGITILMDSEGIKFRPFNGFLKFSGLIDYLQGRIAEDSVVERQKIFKKERRVGIALTKAKVTKEEHFYQVEMLRFSDDCGIAVWVEDGVDFDDEGILGVGGERRFVKFEKREEPECITNLRSKWKKIRDKINETGRLKIYLATPAILGAKGYSSKLDYDLLGDIGIERVRSVNFIGGKPVIFSGWDFVTRKPKPTRYAVPAGSVYFVEFEGEVKLDMPYLKLGKLTKLGYGLCFMGVW

Source

organism	Archaeoglobus fulgidus DSM 4304
ncbi_taxonomy_id	224325
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	CRISPR type III-associated protein domain-containing protein
formula_weight	39677.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,E,F

MFDMFEKAVVFGLYSITPVHAGSGAELSVIDLPIQRERHTGFPVIWGQSLKGVLRSRFRQLELDEKIEVESQKWKWKEKTKEVLKEKADEFIKKVEERKRDPLLTEIVFGPATDGASEHAGAVSVGDAKILLFPVRSAKGVFAFVTSPIVIQRLKEDFELVSEIENDIELKQILSRFKVELSNNETIAGNALILNGENKVILEDIVLKVKSDSNVIENLVEVLKTLFGDNFFGKPIESIKERIAIVSDDVFKSFTRFSTEIVARVRIDAEKGTVARGGLWYEEFLPSDTLMYSLIAVGSPKKENLPKEVDNTQKIVNVLKVTFNNAFLQIGGDETVGKGFVKVRAGVLTGGHKGN

Source

organism	Archaeoglobus fulgidus DSM 4304
ncbi_taxonomy_id	224325
host_organism	Escherichia coli BL21(DE3)

Entity 5 polymer

description	CRISPR system Cmr subunit Cmr5
formula_weight	17407.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,H

MDIREIEQERASFAFKVVSDIKDKYSQNKKVQGKYSSYAEKAPTIILNNGLGATLAFFLSKLEKPIDDVDYKSINPESFGNAENIAYAFLYKHLSTWLAEGNGKDSAFSGLTNGEDPLKYIMEKTAIDVAISTEEALSILNWIKKFAKAMLEEEL

Source

organism	Archaeoglobus fulgidus DSM 4304
ncbi_taxonomy_id	224325
host_organism	Escherichia coli BL21(DE3)

Entity 6 polymer

description	CRISPR type III-associated protein domain-containing protein
formula_weight	40298.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MKSNVVVKYPVNSELANYAEKFWKKELAIYNLSLILNKMTPFVKRRSESYKSSLSAVKEIFKNVDDFQNFLNSVLRRSLDEYRVFFENYERLFNSFSSKIFSMRTKSRLVVGLGDESVYETSIRLHRNYGVPYIPGSALKGVAKHYAFSILARENGDEILRIYESVKEDLKARIAKRDKIKKNDVPEDYYLTAAVIQELFEKKFDELGAIRNTRVEIGDTVISVGDIVKIFGTQKEEGSVIFFDAFPTPEQLKDKPNLELDIMNPHYQPYYQHGEPPGDWHSPNPIFFLTVPAGVEFTFAVASRDLDDLAEKAEKLLKEALKKFGVGAKTSLGYGRFDARDDRHHHHHH

Source

organism	Archaeoglobus fulgidus DSM 4304
ncbi_taxonomy_id	224325
host_organism	Escherichia coli BL21(DE3)

Entity 7 polymer

description	Target analog DNA
formula_weight	9451.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	K

TGCTCTCAGCCGCAAGGACCGCATACTACAA

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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	3.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.40 Å
resolution_method	—
num_particles	81835

fit	/app/data/saxs_computation/x2/9x25/9x25.fit
pddf	/app/data/pr_computation/x2/9x25/9x25.pr.out
profile	/app/data/saxs_computation/x2/9x25/9x25.dat

Target analog-bound type III-B Cmr complex of Archaeoglobus fulgidus

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

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)