SAXSdb — 9z6z

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1. Structure Basics

entry_id	9z6z
deposition_date	2025-11-14
title	Structure of the resting EcDRT3 reverse transcriptase in complex with its non-coding RNA
keywords	DRT3-ncRNA complex, reverse transcriptase, Anti-phage complex, IMMUNE SYSTEM; IMMUNE SYSTEM
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	73.65 Å
rg_electron	69.42 Å
i0	18856100000.00
molecular_weight	999040.0 kDa
excluded_volume	1178800 Å³
envelope_volume	1951600 Å³
shell_volume	220440 Å³
envelope_diameter	222.5 Å
shell_rg	78.45 Å
envelope_rg	68.55 Å
shape_rg	69.23 Å
total_rg	70.06 Å
total_atoms	69342
n_residues	7104
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	268.7 Å
rg_real	76.64 Å
rg_real_error	1.64 Å
i0_real	1.8860e+10
i0_real_error	3.7500e+08
rg_reciprocal	74.70 Å
i0_reciprocal	18910000000.0000
total_estimate	0.8853
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	102.4 Å
skewness	0.487
kurtosis	0.501
angular_range	— – 0.1050 Å⁻¹
current_alpha	0.9610
highest_alpha	1330000000.0000
n_real_points	22
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.653; Stabil: 0.898; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.945

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Drt3a reverse transcriptase protein
formula_weight	50345.8 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	69348

MYDQSFNPRTLSRCFKPEDFQKNRALSLDSVREKTIRAAIERFNNGFLGYNLRSSVLRGKKVYWADELADTLVLRKVQSNLSNLYQLKLPSRTMIVDTLNVFLSECSQYKLYRLDIHSFYESFNKDYIFKKIDELERLEMKTKQLLKEFLYSFYLTGGEGIPRGLSISAYLAELLMHDFDNHLKDDKSVFYYARYVDDIVIVTSGFEDSNAFIENVKSILPPGLSFNEGEKYYISDLIPKSANKKNTHHHHHHESPTKLLTFEYLGYDFSVGDKIEECNIRGFYRLIEVDLAHAKANKIKSRIIYSIIDYNKTKDFELLCERLKFLSTNFSILDSGRVLKRLSGIHYNYPLVDARTSRRLAELDLFLRKAVLSSNGKVFFDFHANLNQYKKYRLLKISFVRGHEKRHFFHYSASKMMRIQRCWKYV

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 polymer

description	Drt3b reverse transcriptase protein
formula_weight	76426.6 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	H,I,J,K,L,M

MSKKKEVRVNKKDFNRVLVTETIPYETPIIVSNDGFYNNVVKHQTANDIAKLLTQRVILGERKKGRYTIPYVFKINKNETEFRRLAFPHPISQIEMRDFYLHFNQVMINFCSKSDFSIRRPVKVASTYYYKNLLEDKNLYKRGPVDTDKNELLTRHASSYFGYHGYDRLYKFFMSNDFIDLERKYNTLYTLDVSKCFDSIYTHSISWATKTKTFTKGMLANKSLNFGDAFDKLMQRCNFNETHGVIIGPEISRIFAEIIFQKIDLNVQFKLRNIDTPLNKGVDYDIRRYVDDVFIFSKNEVNAEIIYKVYADKLNEYNMHVNLGKVTKNSRPFITAKTQIIHHVNQKMNVFIDSFLSYDDEMKLIAKPIYNNRKLANKFIDEVKIICSERKSGYGEVSSYIVSAIFERIKRLTSSVNQAEDKDIYNVMYVLLHISLFFFRVAPSVSSSYKLASILIVTLRYFKAQVPSYSDLIASYIYFEIEDFLKAAKNGKKTIDNLVSLEAYNIMYVIGELDQDRYLSKQLVEDVFSEVDSYFDIVSCLYIVKDKKVYDSLKNNIIDVINSKLMSSDNILDYSEKAMLFLDVMSCPYIDLKWKKIWLKSILKELQEATPNNNEIDSFISYSVANPWFVDWSNVDLLNFLEKKQLKKAY

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 3 polymer

description	non-coding RNA
formula_weight	44236.2 kDa
src_method	man
entity_count	6

Polymer

type	polyribonucleotide
strand_id	R,S,T,U,V,W

AAUGCAACCAAUAUGCCCUACACGAUUUUUCGAUAUACUAGGGCUGAUUACGGUAGGUAAGUUACACGUAACCUUAGCUACCUUAUGACGCUCAAGAGCAGCAAUGCACACACUAAGGGAUGAGGUUGCUUCAAUUUC

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 4 polymer

description	;DNA (5'-D(PTPGPTPGP*T)-3') ;
formula_weight	3730.4 kDa
src_method	man
entity_count	6

Polymer

type	polydeoxyribonucleotide
strand_id	X,Z,b,d,f,h

TGTGTGTTGTGT

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 5 polymer

description	;DNA (5'-D(PAPCPAPCPAPCPAPCPAPCPAPCPAPCPAPCP*A)-3') ;
formula_weight	5087.4 kDa
src_method	man
entity_count	6

Polymer

type	polydeoxyribonucleotide
strand_id	Y,a,c,e,g,i

ACACACACACACACACA

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	6

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	6

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6. Citations (1)

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resolution	2.60 Å
resolution_method	—
num_particles	63349

fit	/app/data/saxs_computation/z6/9z6z/9z6z.fit
pddf	/app/data/pr_computation/z6/9z6z/9z6z.pr.out
profile	/app/data/saxs_computation/z6/9z6z/9z6z.dat

Structure of the resting EcDRT3 reverse transcriptase in complex with its non-coding RNA

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)