SAXSdb — 9vj9

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1. Structure Basics

entry_id	9vj9
deposition_date	2025-06-19
title	Type I-A CRISPR integrase prespacer catching complex, State I
keywords	CRISPR, Cas9, Cas1, Csn2 DNA binding protein, DNA BINDING PROTEIN/DNA/RNA, DNA BINDING PROTEIN-DNA-RNA complex; DNA BINDING PROTEIN/DNA/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	54.22 Å
rg_electron	53.93 Å
i0	2336390000.00
molecular_weight	377890.0 kDa
excluded_volume	461660 Å³
envelope_volume	702980 Å³
shell_volume	108240 Å³
envelope_diameter	171.2 Å
shell_rg	57.64 Å
envelope_rg	51.93 Å
shape_rg	53.93 Å
total_rg	54.04 Å
total_atoms	26415
n_residues	2949
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	169.4 Å
rg_real	54.06 Å
rg_real_error	0.86 Å
i0_real	2.3360e+09
i0_real_error	3.4000e+07
rg_reciprocal	54.33 Å
i0_reciprocal	2337000000.0000
total_estimate	0.8733
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.3 Å
skewness	0.164
kurtosis	-0.627
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0002
highest_alpha	265200000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.486

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Type II-A CRISPR-associated protein Csn2
formula_weight	25433.1 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,C,D,A
atom_count	26415

MRVNFSLLEEPIEIEKATFLTIKDVQTFAHLVKLIYQYDGENELKLFDAQQKGLKPTELFVVTDILGYDVNSAATLKLIYGDLEAQLNDKPEVKSMIEKLTGTISQLIGYELLEHEMDLEEDGITVQELFKALGIKIETTSDTIFEKVMEITQVHRYLSKKKLLIFINACTYLTEDEVQQVVEYISLNNVDVLFLEQRVVQNRFQYILDENFYLSYEKA

Source

organism	Enterococcus faecalis
ncbi_taxonomy_id	1351
host_organism	Escherichia coli

Entity 2 polymer

description	CRISPR-associated endonuclease Cas1
formula_weight	33492.6 kDa
ec_number	3.1.-.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,L

MGWRTVVVNKHSKLSYKNNHLVFKAIDHQELIHLSEIDVLLLETTDISLTTMLLKRLIDEKILVLFCDDKRLPIGKILPFYGRHDSSLQLTRQLAWTEERKGQVWTAIIAQKITNQSLHLAQRDYGQKAAALLAMRAELRLFDPANREGHAARSYFNTLFGNDFTREQENDINAGLNYGYTLLLSIFARELVQTGCFTQLGLKHANQFNDFNLASDLMEPFRPLVDQIIYENRKEAFPIMKRKLFALFMNTYMYKKKQMFLTNIATDYTKHVVKVLNQEEEGVPEFGI

Source

organism	Enterococcus faecalis
ncbi_taxonomy_id	1351
host_organism	Escherichia coli

Entity 3 polymer

description	DNA (51-MER)
formula_weight	15774.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	N

AGCGCTCTGAATGCTAGATCACGTTATGAAACAGACATAGCGGTACAAAAA

Entity 4 polymer

description	DNA (51-MER)
formula_weight	15644.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

TTTTTGTACCGCTATGTCTGTTTCATAACGTGATCTAGCATTCAGAGCGCT

Entity 5 polymer

description	RNA (55-MER)
formula_weight	17561.3 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	g

GCAAUACUUUGUCUGUAUCGUUUUAGAGUCAUGUUGUUUAGAAUGGUACCAAAAC

Entity 6 polymer

description	RNA (83-MER)
formula_weight	26614.8 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	t

CUUUUGGGACUAUUCUAAACAACAUAGCAAGUUAAAAUAAGGUUUUAACCGUAAUCAACUGUAAAGUGGCGCUGUUUCGGCGC

Entity 7 polymer

description	CRISPR-associated endonuclease Cas9
formula_weight	155565.3 kDa
ec_number	3.1.-.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	S

MKKDYVIGLDIGTNSVGWAVMTEDYQLVKKKMPIYGNTEKKKIKKNFWGVRLFEEGHTAEDRRLKRTARRRISRRRNRLRYLQAFFEEAMTDLDENFFARLQESFLVPEDKKWHRHPIFAKLEDEVAYHETYPTIYHLRKKLADSSEQADLRLIYLALAHIVKYRGHFLIEGKLSTENISVKEQFQQFMIIYNQTFVNGESRLVSAPLPESVLIEEELTEKASRTKKSEKVLQQFPQEKANGLFGQFLKLMVGNKADFKKVFGLEEEAKITYASESYEEDLEGILAKVGDEYSDVFLAAKNVYDAVELSTILADSDKKSHAKLSSSMIVRFTEHQEDLKKFKRFIRENCPDEYDNLFKNEQKDGYAGYIAHAGKVSQLKFYQYVKKIIQDIAGAEYFLEKIAQENFLRKQRTFDNGVIPHQIHLAELQAIIHRQAAYYPFLKENQEKIEQLVTFRIPYYVGPLSKGDASTFAWLKRQSEEPIRPWNLQETVDLDQSATAFIERMTNFDTYLPSEKVLPKHSLLYEKFMVFNELTKISYTDDRGIKANFSGKEKEKIFDYLFKTRRKVKKKDIIQFYRNEYNTEIVTLSGLEEDQFNASFSTYQDLLKCGLTRAELDHPDNAEKLEDIIKILTIFEDRQRIRTQLSTFKGQFSAEVLKKLERKHYTGWGRLSKKLINGIYDKESGKTILGYLIKDDGVSKHYNRNFMQLINDSQLSFKNAIQKAQSSEHEETLSETVNELAGSPAIKKGIYQSLKIVDELVAIMGYAPKRIVVEMARENQTTSTGKRRSIQRLKIVEKAMAEIGSNLLKEQPTTNEQLRDTRLFLYYMQNGKDMYTGDELSLHRLSHYDIDHIIPQSFMKDDSLDNLVLVGSTENRGKSDDVPSKEVVKDMKAYWEKLYAAGLISQRKFQRLTKGEQGGLTLEDKAHFIQRQLVETRQITKNVAGILDQRYNANSKEKKVQIITLKASLTSQFRSIFGLYKVREVNDYHHGQDAYLNCVVATTLLKVYPNLAPEFVYGEYPKFQTFKENKATAKAIIYTNLLRFFTEDEPRFTKDGEILWSNSYLKTIKKELNYHQMNIVKKVEVQKGGFSKESIKPKGPSNKLIPVKNGLDPQKYGGFDSPIVAYTVLFTHEKGKKPLIKQEILGITIMEKTRFEQNPILFLEEKGFLRPRVLMKLPKYTLYEFPEGRRRLLASAKEAQKGNQMVLPEHLLTLLYHAKQCLLPNQSESLAYVEQHQPEFQEILERVVDFAEVHTLAKSKVQQIVKLFEANQTADVKEIAASFIQLMQFNAMGAPSTFKFFQKDIERARYTSIKEIFDATIIYQSTTGLYETRRKVVD

Source

organism	Enterococcus faecalis
ncbi_taxonomy_id	1351
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	2.960 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.96 Å
resolution_method	—
num_particles	136878

fit	/app/data/saxs_computation/vj/9vj9/9vj9.fit
pddf	/app/data/pr_computation/vj/9vj9/9vj9.pr.out
profile	/app/data/saxs_computation/vj/9vj9/9vj9.dat

Type I-A CRISPR integrase prespacer catching complex, State I

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

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)