SAXSdb — 9yfd

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1. Structure Basics

entry_id	9yfd
deposition_date	2025-09-25
title	Defense-associated reverse transcriptase 1 (DRT1) filament
keywords	Anti-phage defense, DNA synthesis, Nitrilase domain, RT domain, filament, ANTIVIRAL PROTEIN; ANTIVIRAL 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	71.03 Å
rg_electron	70.63 Å
i0	14709500000.00
molecular_weight	1041600.0 kDa
excluded_volume	1307200 Å³
envelope_volume	2056600 Å³
shell_volume	230310 Å³
envelope_diameter	221.1 Å
shell_rg	80.01 Å
envelope_rg	67.71 Å
shape_rg	70.62 Å
total_rg	70.76 Å
total_atoms	73480
n_residues	9000
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	225.8 Å
rg_real	70.70 Å
rg_real_error	1.74 Å
i0_real	1.4710e+10
i0_real_error	3.3580e+08
rg_reciprocal	72.06 Å
i0_reciprocal	14750000000.0000
total_estimate	0.8599
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	92.4 Å
skewness	0.065
kurtosis	-0.537
angular_range	— – 0.1100 Å⁻¹
current_alpha	0.0000
highest_alpha	1004000000.0000
n_real_points	23
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.686

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Defense-associated reverse transcriptase 1
formula_weight	141552.0 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	73480

MKLLNKKYYNLEPNFDYLKDSFILGLAWKKTDRFVRTHNWYADLLALDKCAFDISDEVTSWSSEAVNRNLSKSDIELIPAPKRASWFFNKGKWTTNKDDRKLRPLANISIKDQSFATAVTMCLADAIETRQKDCSLRNLGYAEHVNKKVVSYGNRLVCDWDNERARFRWGGSEYYRKFSTDYRNFLQRPVYIGRETVNKISEIDDVYIISLDLKNFFGSIKISTLLEKLKKISSDHYDHNIINENEFWGLASQILNWEWPEDSLSLLKNLDIEEENVGLPQGLASAGALANAYLIEFDESLTSNLRTKIDGSQIVLHDYCRYVDDIRLVISGEALTNEEIKKSIHELVQRILDETLDQDESDNEPYLKINDKKTYILGLSDIDNGSSLTNRINEIQNEVGTSSIPERNGLDNNIPALQQLLLTEQDNFLEDADGLFSGFNNDKSIKLESLRRFSAHRLETSLANKSKLISPAERKQFDNESALIAKKLLKTWLKDPSIMVIFRKAITINPNLDAYKTILEIIFLRIQHNREKCDRYIMLYLLSDIFRSVVDIYRKLSPECTSDYQKLMSEVTSFAHKLLSCRSVIPNYAYQQALFYLAVINKPFIASKKSSSDLSKLQHVLIKRHLEPLSSSDGYLFELSAQISKDYQANVAFLLSHTNTTEVVDSIVEKFAYRGGEFWNSIWKEFVRTKDKVRINKFRWAIPKNESKPNGSDHYLSSVISFKENPFKYEHALLKLGIALVNLLEDTEKNVWQSDGKQYSPHEIKVKLEGHSTSWTELWRQNSIISCSIDKIAQDPRYESPKWLVNCQQAKNDEKKIYWVCSVLRSAALGNVDYTQRNDLKPDRVEYDGIHSQFYKRRMGMLHTPESIVGSYATITDWFASFLQHGLQWPGFSSSYINQEDILSITSLGEFKKCLLERLGYLNTQICTSSSVPTLPTVVNRPELASNYFRIVTVQQLFPKDKHFHPSDVTLDNPEVRWKHREHLAEICKLTEQTLDAKLKTESRDHTSTADLIVFSELAVHPEDEDIVRALAFRTRSIIFCGFVFCEQDGQIVNKARWIIPDSSESGTQWRVRDQGKFHMTSGEMSLGVHGYRPSQHIISIEGHTEGPFKLTGAICYDATDIKLAADLRDLTDMFVIAAYNKDVDTFDNMASALQWHMYQHVIITNTGEYGGSTMQAPYKEKHHKLISHAHGTGQIAISTADIDLAAFRRKIKEYKKTKTQPAGFKRKH

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 non-polymer

description	;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ;
formula_weight	491.2 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	16

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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	2.60 Å
resolution_method	—
num_particles	140634

fit	/app/data/saxs_computation/yf/9yfd/9yfd.fit
pddf	/app/data/pr_computation/yf/9yfd/9yfd.pr.out
profile	/app/data/saxs_computation/yf/9yfd/9yfd.dat

Defense-associated reverse transcriptase 1 (DRT1) filament

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