SAXSdb — 9vjb

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1. Structure Basics

entry_id	9vjb
deposition_date	2025-06-19
title	Type II-A CRISPR integrase pre-integration complex
keywords	CRISPR, Cas1, Cas2, Csn2, DNA BINDING PROTEIN/DNA, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/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	44.75 Å
rg_electron	44.76 Å
i0	528124000.00
molecular_weight	187050.0 kDa
excluded_volume	233220 Å³
envelope_volume	337630 Å³
shell_volume	64537 Å³
envelope_diameter	152.0 Å
shell_rg	47.81 Å
envelope_rg	43.55 Å
shape_rg	44.80 Å
total_rg	44.74 Å
total_atoms	13115
n_residues	1529
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	148.6 Å
rg_real	44.77 Å
rg_real_error	1.60 Å
i0_real	5.2810e+08
i0_real_error	1.0100e+07
rg_reciprocal	44.75 Å
i0_reciprocal	528100000.0000
total_estimate	0.8888
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.7 Å
skewness	0.312
kurtosis	-0.530
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	60670000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.884

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

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	A,B,C,D
atom_count	13115

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	I,J

MGWRTVVVNKHSKLSYKNNHLVFKAIDHQELIHLSEIDVLLLETTDISLTTMLLKRLIDEKILVLFCDDKRLPIGKILPFYGRHDSSLQLTRQLAWTEERKGQVWTAIIAQKITNQSLHLAQRDYGQKAAALLAMRAELRLFDPANREGHAARSYFNTLFGNDFTREQENDINAGLNYGYTLLLSIFARELVQTGCFTQLGLKHANQFNDFNLASDLMEPFRPLVDQIIYENRKEAFPIMKRKLFALFMNTYMYKKKQMFLTNIATDYTKHVVKVLNQEEEGVPEFGI

Source

organism	Enterococcus faecalis
ncbi_taxonomy_id	1351
host_organism	Escherichia coli

Entity 3 polymer

description	DNA (51-MER)
formula_weight	15468.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	X

TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Entity 4 polymer

description	DNA (51-MER)
formula_weight	15928.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	Y

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Entity 5 polymer

description	CRISPR-associated endoribonuclease Cas2
formula_weight	12977.0 kDa
ec_number	3.1.-.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

MSYRYMRLLLMFDMPTDTASDRKAYRKFRKFLINEGFIMHQFSVYSKILLNDTANKAMLARLKQNNPQRGLITLLNVTEKQFSRMIYLHGEQDNRVANSDERIVFLGEE

Source

organism	Enterococcus faecalis
ncbi_taxonomy_id	1351
host_organism	Escherichia coli

Entity 6 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	6

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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	3.760 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.76 Å
resolution_method	—
num_particles	50477

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

Type II-A CRISPR integrase pre-integration complex

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)