SAXSdb — 9z6y

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1. Structure Basics

entry_id	9z6y
deposition_date	2025-11-14
title	Structure of the elongating 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	73.60 Å
rg_electron	69.55 Å
i0	19827800000.00
molecular_weight	1018500.0 kDa
excluded_volume	1199200 Å³
envelope_volume	1964200 Å³
shell_volume	221560 Å³
envelope_diameter	225.6 Å
shell_rg	78.69 Å
envelope_rg	68.55 Å
shape_rg	69.36 Å
total_rg	70.17 Å
total_atoms	70608
n_residues	7128
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	270.0 Å
rg_real	76.78 Å
rg_real_error	1.51 Å
i0_real	1.9840e+10
i0_real_error	4.0860e+08
rg_reciprocal	74.68 Å
i0_reciprocal	19880000000.0000
total_estimate	0.8820
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	102.9 Å
skewness	0.502
kurtosis	0.566
angular_range	— – 0.1050 Å⁻¹
current_alpha	0.9624
highest_alpha	1315000000.0000
n_real_points	22
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.636; Stabil: 0.890; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.958

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

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	70614

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	;cDNA (5'-D(PTPGPTPGPTPGPTPGPTPGPTPGPTPGPTPGP*T)-3') ;
formula_weight	5326.4 kDa
src_method	man
entity_count	6

Polymer

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

TGTGTGTGTGTGTGTGT

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 5 polymer

description	;cDNA (5'-D(PCPAPCPAPCPAPCPAPCPAPCPAPCPAPCPAPCPA)-3') ;
formula_weight	5376.5 kDa
src_method	man
entity_count	6

Polymer

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

CACACACACACACACACA

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	18

Entity 7 non-polymer

description	PYROPHOSPHATE 2-
formula_weight	176.0 kDa
src_method	syn
entity_count	6

Entity 8 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	239792

fit	/app/data/saxs_computation/z6/9z6y/9z6y.fit
pddf	/app/data/pr_computation/z6/9z6y/9z6y.pr.out
profile	/app/data/saxs_computation/z6/9z6y/9z6y.dat

Structure of the elongating 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 (8)

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 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)