SAXSdb — 9vj8

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1. Structure Basics

entry_id	9vj8
deposition_date	2025-06-19
title	Type II-A CRISPR integrase complex, apo form
keywords	CRISPR, Cas9, Cas1, Cas2, Csn2, DNA BINDING PROTEIN; DNA 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	69.40 Å
rg_electron	68.58 Å
i0	3513650000.00
molecular_weight	524570.0 kDa
excluded_volume	666300 Å³
envelope_volume	1162700 Å³
shell_volume	143550 Å³
envelope_diameter	216.0 Å
shell_rg	70.12 Å
envelope_rg	64.78 Å
shape_rg	68.62 Å
total_rg	68.48 Å
total_atoms	36995
n_residues	4512
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	234.0 Å
rg_real	69.22 Å
rg_real_error	2.11 Å
i0_real	3.5140e+09
i0_real_error	7.7820e+07
rg_reciprocal	69.93 Å
i0_reciprocal	3518000000.0000
total_estimate	0.8451
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	91.6 Å
skewness	0.151
kurtosis	-0.352
angular_range	— – 0.1150 Å⁻¹
current_alpha	0.0002
highest_alpha	192900000.0000
n_real_points	24
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.607

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Type II-A CRISPR-associated protein Csn2
formula_weight	25433.1 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	36995

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	8

Polymer

type	polypeptide(L)
strand_id	I,J,K,L,O,P,Q,R

MGWRTVVVNKHSKLSYKNNHLVFKAIDHQELIHLSEIDVLLLETTDISLTTMLLKRLIDEKILVLFCDDKRLPIGKILPFYGRHDSSLQLTRQLAWTEERKGQVWTAIIAQKITNQSLHLAQRDYGQKAAALLAMRAELRLFDPANREGHAARSYFNTLFGNDFTREQENDINAGLNYGYTLLLSIFARELVQTGCFTQLGLKHANQFNDFNLASDLMEPFRPLVDQIIYENRKEAFPIMKRKLFALFMNTYMYKKKQMFLTNIATDYTKHVVKVLNQEEEGVPEFGI

Source

organism	Enterococcus faecalis
ncbi_taxonomy_id	1351
host_organism	Escherichia coli

Entity 3 polymer

description	CRISPR-associated endoribonuclease Cas2
formula_weight	12977.0 kDa
ec_number	3.1.-.-
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	M,N,U,V

MSYRYMRLLLMFDMPTDTASDRKAYRKFRKFLINEGFIMHQFSVYSKILLNDTANKAMLARLKQNNPQRGLITLLNVTEKQFSRMIYLHGEQDNRVANSDERIVFLGEE

Source

organism	Enterococcus faecalis
ncbi_taxonomy_id	1351
host_organism	Escherichia coli

Entity 4 polymer

description	CRISPR-associated endonuclease Cas9
formula_weight	155565.3 kDa
ec_number	3.1.-.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	S,T

MKKDYVIGLDIGTNSVGWAVMTEDYQLVKKKMPIYGNTEKKKIKKNFWGVRLFEEGHTAEDRRLKRTARRRISRRRNRLRYLQAFFEEAMTDLDENFFARLQESFLVPEDKKWHRHPIFAKLEDEVAYHETYPTIYHLRKKLADSSEQADLRLIYLALAHIVKYRGHFLIEGKLSTENISVKEQFQQFMIIYNQTFVNGESRLVSAPLPESVLIEEELTEKASRTKKSEKVLQQFPQEKANGLFGQFLKLMVGNKADFKKVFGLEEEAKITYASESYEEDLEGILAKVGDEYSDVFLAAKNVYDAVELSTILADSDKKSHAKLSSSMIVRFTEHQEDLKKFKRFIRENCPDEYDNLFKNEQKDGYAGYIAHAGKVSQLKFYQYVKKIIQDIAGAEYFLEKIAQENFLRKQRTFDNGVIPHQIHLAELQAIIHRQAAYYPFLKENQEKIEQLVTFRIPYYVGPLSKGDASTFAWLKRQSEEPIRPWNLQETVDLDQSATAFIERMTNFDTYLPSEKVLPKHSLLYEKFMVFNELTKISYTDDRGIKANFSGKEKEKIFDYLFKTRRKVKKKDIIQFYRNEYNTEIVTLSGLEEDQFNASFSTYQDLLKCGLTRAELDHPDNAEKLEDIIKILTIFEDRQRIRTQLSTFKGQFSAEVLKKLERKHYTGWGRLSKKLINGIYDKESGKTILGYLIKDDGVSKHYNRNFMQLINDSQLSFKNAIQKAQSSEHEETLSETVNELAGSPAIKKGIYQSLKIVDELVAIMGYAPKRIVVEMARENQTTSTGKRRSIQRLKIVEKAMAEIGSNLLKEQPTTNEQLRDTRLFLYYMQNGKDMYTGDELSLHRLSHYDIDHIIPQSFMKDDSLDNLVLVGSTENRGKSDDVPSKEVVKDMKAYWEKLYAAGLISQRKFQRLTKGEQGGLTLEDKAHFIQRQLVETRQITKNVAGILDQRYNANSKEKKVQIITLKASLTSQFRSIFGLYKVREVNDYHHGQDAYLNCVVATTLLKVYPNLAPEFVYGEYPKFQTFKENKATAKAIIYTNLLRFFTEDEPRFTKDGEILWSNSYLKTIKKELNYHQMNIVKKVEVQKGGFSKESIKPKGPSNKLIPVKNGLDPQKYGGFDSPIVAYTVLFTHEKGKKPLIKQEILGITIMEKTRFEQNPILFLEEKGFLRPRVLMKLPKYTLYEFPEGRRRLLASAKEAQKGNQMVLPEHLLTLLYHAKQCLLPNQSESLAYVEQHQPEFQEILERVVDFAEVHTLAKSKVQQIVKLFEANQTADVKEIAASFIQLMQFNAMGAPSTFKFFQKDIERARYTSIKEIFDATIIYQSTTGLYETRRKVVD

Source

organism	Enterococcus faecalis
ncbi_taxonomy_id	1351
host_organism	Escherichia coli

Entity 5 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	12

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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	3.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.90 Å
resolution_method	—
num_particles	52810

fit	/app/data/saxs_computation/vj/9vj8/9vj8.fit
pddf	/app/data/pr_computation/vj/9vj8/9vj8.pr.out
profile	/app/data/saxs_computation/vj/9vj8/9vj8.dat

Type II-A CRISPR integrase complex, apo form

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)