SAXSdb — 9zs4

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1. Structure Basics

entry_id	9zs4
deposition_date	2025-12-22
title	S. marcescens Cas10-Csm bound to target RNA
keywords	CRISPR, crRNA, Cas10, type III, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	56.03 Å
rg_electron	57.10 Å
i0	1828300000.00
molecular_weight	340340.0 kDa
excluded_volume	419080 Å³
envelope_volume	614790 Å³
shell_volume	92902 Å³
envelope_diameter	205.9 Å
shell_rg	54.95 Å
envelope_rg	57.46 Å
shape_rg	57.11 Å
total_rg	57.02 Å
total_atoms	23910
n_residues	2930
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	194.1 Å
rg_real	56.57 Å
rg_real_error	2.19 Å
i0_real	1.8280e+09
i0_real_error	3.6390e+07
rg_reciprocal	55.57 Å
i0_reciprocal	1826000000.0000
total_estimate	0.7883
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	48.5 Å
skewness	0.588
kurtosis	-0.287
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	545900000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.677; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.861; Smooth: 0.353

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
formula_weight	90390.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	23910

MNWLAASCHVAAFALLHNLKPLAQRAGIQDFPSPALANKLFAPLPESLSARADLHENTLTLLLDFAARLARGLPETPVSRGETGLIPLTHLLADDNHSAPAERCYSPLAPLGVDSLMPVTAALPTGERQAAYRQVYQALIEGLEAIPAAHRLQPSLWLDHLDSLWMTTCHALPDGDGASGISLYDQGKTTAALAVALWQHHARQATPEKEISLTPGDDARLLLIQADVFGIQELIFAQGNQTQKMAAKLLRGRSFQVSLLAETAALRVLETFDLPPVCQLINAAGKSLIVAPNLPDAAERLAGLRQRLDEWFLTHTYAQTGIGLCSTVAGSAEFLGEQAYGRLQNRLAQAMEQQKYQRFSLCAGDAPPPVFEGYLDQIAQGAGGEPCPMNGLHPVETTLNGLGCSRLAADQITLGHWINHGHWISHGERYARLLILRDSTATFSDDRCLHLTLFGYQVVAVSLKEDSGEFGELACNGSLRRCWDVSLPPEGTSLFQGYARRFINGWMPLAQGEYQPECYPGIEEALANGDIKTFDHLSCEDLYQDADQSLRGTCALGVLKGDIDNLGHLFRSGLPQPGFAKTIGLSRQIHLFFTLWLPHLCRKDPRFANTYTVFAGGDDFFLIGPWRSQQTLALTMAQDFARYSGHNPALHFSLGLVQAKPGYPVRALAAQAEAALKQAKQHPGKNAICLYNEVMGWPEYDALLACSEELARWREHDGYPLSSGLLYRLLALSEQSAEESEKPQAALWRSRLAYFLRRNLVDNVKVPTKENPAAFRHQLHLELFEKLEQHLKRHRQRYRVALQRHLYHYRTVPRGE

Source

organism	Serratia
ncbi_taxonomy_id	613
host_organism	Escherichia coli

Entity 2 polymer

description	crRNA
formula_weight	13361.9 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	K

AUUAAGACCAUUUACAGAACCUGUUCCACUUAAUGAAGUUGC

Entity 3 polymer

description	Target RNA
formula_weight	13560.1 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	L

GCAACUUCAUUAAGUGGAACAGGUUCUGUAAAUGCGGAAGUA

Entity 4 polymer

description	CRISPR system Cms protein Csm2
formula_weight	15886.1 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,C,D

MHHHHHHTTLDYFKRQLHKPEATFFDDDAQKFAEQLAQYGKKGKPTQLRRFYDQLQQLEQRINGDEEKLALYLPEIRMISAHLAYAKGRELISDEFCQTMQNLIRSINTCQHLKNGRLFFEATLGFLRAIRRD

Source

organism	Serratia
ncbi_taxonomy_id	613
host_organism	Escherichia coli

Entity 5 polymer

description	CRISPR system Cms endoribonuclease Csm3
formula_weight	27185.9 kDa
mutation	D34A
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	E,F,G,H

MQLNNIQTLRATLVCETGLHIGGGDTALQIGGIASAVVRHPLTQQPYIPGSSLKGKLRSLLEWRAGVVGDTEGKVLSHQVYQQLIDDKKQAQALQALKILQLFGVSGGDKLSAEQAQQIGPTRLSFWDCEFDEHWLAQQGGRVQTEEKAENCIDRISGVALHPRFIERVPAGSRFDFRLTVRQLDGDSPDLLDTLLAGLKMLELDGLGGSISRGYGKVRFEALTLDGKDLQPRFEQLQPFKHTTQGAG

Source

organism	Serratia
ncbi_taxonomy_id	613
host_organism	Escherichia coli

Entity 6 polymer

description	CRISPR system Cms protein Csm4
formula_weight	35770.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MPSPVAPAAAWQWLRLRLLPDSAFATALRGDTLFGQLCWYLRESLGEAGLNALLAGYHDQRPFAVISDPMLADHLPRPHLPEHRLGFAAADARARKQRKQQCWLPLAFAHQPLAEWGAHLTAAPEHHQHRSDVQMHNSINRQTLTTGGDDAFAPFGSEQHWFDVDTAWDLYLLHDKRLSAAQLTDALRAIGLLGYGKDASIGKGRFHLTPQPMPELPTPDGNPLRLTLAPCAPQQGHWHSADSFFSPLVRVGRHGAALVVQGHPFKNPLLLADSAAVLAPVTPDNRPFVGQGLGGNGRLSTALPQTVHQGYAPVIPVRFHHKAQPQ

Source

organism	Serratia
ncbi_taxonomy_id	613
host_organism	Escherichia coli

Entity 7 polymer

description	CRISPR system Cms protein Csm5
formula_weight	63148.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MTRDQTPRRHTACDSDNMQYFTLTCLSPVHVATGDSLNPGEYLIDENALYELGQGGLSPALTATQRSELLTILESNDPALPLTVQRFLAREAGKLKYAARRMCPLLPGISRYYQSRLGQVMQNDTKNKKQMINQLELMRHVGAALGAPYIPGSTLKGAIRTALVSALNQGQPLQAERRETDKLSSKVAQDAERQLLGFDTRRDSPRYRIEHDPFHWLQVGDAVSPAEHPPMLDYWLVRRQPFKRTEKQDNKADNMELSPVECLKPRQSPLHCQITVKTPPTALAIKNPRLKQWLGKVSQLAQQVNRITLPQCHHELAWLAEKHIGTDDVYAPGQNWVAQMQQLLRQLDDPLQRGEALLLRVGKYGGAISKTVAGWRHIARLGRQGTRTTYHPDVTTCTLALPQADALTQALPFGWVLLHQPDQPEVTEFVASHHDWCQQQQQRLDAHQQQQHTHRQQRQQLAQAREEEAQRLADKARQSKARQSIMSLAEQLASEQTFQHKNPNGPLRGQLATCVGCVATEGSAEEKAELCTLFDDILNYWGIKPGKDKKLTALRNKLL

Source

organism	Serratia
ncbi_taxonomy_id	613
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	triclinic

resolution	3.80 Å
resolution_method	—
num_particles	129762

fit	/app/data/saxs_computation/zs/9zs4/9zs4.fit
pddf	/app/data/pr_computation/zs/9zs4/9zs4.pr.out
profile	/app/data/saxs_computation/zs/9zs4/9zs4.dat

S. marcescens Cas10-Csm bound to target RNA

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)