SAXSdb — 9vja

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1. Structure Basics

entry_id	9vja
deposition_date	2025-06-19
title	Type I-A CRISPR integrase prespacer catching complex, State II
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	54.86 Å
rg_electron	54.53 Å
i0	2347350000.00
molecular_weight	378070.0 kDa
excluded_volume	461630 Å³
envelope_volume	707730 Å³
shell_volume	108550 Å³
envelope_diameter	174.3 Å
shell_rg	57.28 Å
envelope_rg	52.61 Å
shape_rg	54.53 Å
total_rg	54.62 Å
total_atoms	26425
n_residues	2950
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	177.0 Å
rg_real	54.71 Å
rg_real_error	1.29 Å
i0_real	2.3470e+09
i0_real_error	4.5780e+07
rg_reciprocal	54.96 Å
i0_reciprocal	2348000000.0000
total_estimate	0.8888
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	61.0 Å
skewness	0.170
kurtosis	-0.638
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0002
highest_alpha	244200000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.770

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 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
atom_count	26425

MGWRTVVVNKHSKLSYKNNHLVFKAIDHQELIHLSEIDVLLLETTDISLTTMLLKRLIDEKILVLFCDDKRLPIGKILPFYGRHDSSLQLTRQLAWTEERKGQVWTAIIAQKITNQSLHLAQRDYGQKAAALLAMRAELRLFDPANREGHAARSYFNTLFGNDFTREQENDINAGLNYGYTLLLSIFARELVQTGCFTQLGLKHANQFNDFNLASDLMEPFRPLVDQIIYENRKEAFPIMKRKLFALFMNTYMYKKKQMFLTNIATDYTKHVVKVLNQEEEGVPEFGI

Source

organism	Enterococcus faecalis
ncbi_taxonomy_id	1351
host_organism	Escherichia coli

Entity 2 polymer

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

Polymer

type	polydeoxyribonucleotide
strand_id	N

AGCGCTCTGAATGCTAGATCACGTTATGAAACAGACATAGCGGTACAAAAA

Entity 3 polymer

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

Polymer

type	polydeoxyribonucleotide
strand_id	T

TTTTTGTACCGCTATGTCTGTTTCATAACGTGATCTAGCATTCAGAGCGCT

Entity 4 polymer

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

Polymer

type	polyribonucleotide
strand_id	g

GCAAUACUUUGUCUGUAUCGUUUUAGAGUCAUGUUGUUUAGAAUGGUACCAAAAC

Entity 5 polymer

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

Polymer

type	polyribonucleotide
strand_id	t

CUUUUGGGACUAUUCUAAACAACAUAGCAAGUUAAAAUAAGGUUUUAACCGUAAUCAACUGUAAAGUGGCGCUGUUUCGGCGC

Entity 6 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	A,B,C,D

MRVNFSLLEEPIEIEKATFLTIKDVQTFAHLVKLIYQYDGENELKLFDAQQKGLKPTELFVVTDILGYDVNSAATLKLIYGDLEAQLNDKPEVKSMIEKLTGTISQLIGYELLEHEMDLEEDGITVQELFKALGIKIETTSDTIFEKVMEITQVHRYLSKKKLLIFINACTYLTEDEVQQVVEYISLNNVDVLFLEQRVVQNRFQYILDENFYLSYEKA

Source

organism	Enterococcus faecalis
ncbi_taxonomy_id	1351
host_organism	Escherichia coli

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	3.010 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.01 Å
resolution_method	—
num_particles	80591

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

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

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

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)