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9vdo

Cryo-EM structure of the substrate bound DRT4

Method: ELECTRON MICROSCOPY D_max: 138.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vdo
deposition_date	2025-06-09
title	Cryo-EM structure of the substrate bound DRT4
keywords	UG15, DRT4, Reverse transcriptases, UG/Abi system, 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	45.16 Å
rg_electron	44.76 Å
i0	1906000000.00
molecular_weight	356560.0 kDa
excluded_volume	442630 Å³
envelope_volume	573090 Å³
shell_volume	101880 Å³
envelope_diameter	134.8 Å
shell_rg	53.14 Å
envelope_rg	43.65 Å
shape_rg	44.82 Å
total_rg	44.86 Å
total_atoms	25026
n_residues	2994
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	138.7 Å
rg_real	44.83 Å
rg_real_error	0.86 Å
i0_real	1.9060e+09
i0_real_error	3.4590e+07
rg_reciprocal	45.15 Å
i0_reciprocal	1907000000.0000
total_estimate	0.8982
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	59.5 Å
skewness	0.050
kurtosis	-0.587
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	320500000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.924

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Reverse transcriptase domain-containing protein
formula_weight	63911.0 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,D,F,H,K
atom_count	25026

HHHHHHSSGMVIFDEKRHLYEALLRHNYFPNQKGSISEIPPCFSSRTFTPEIAELISSDTSGRRSLQGYDCVEYYATRYNNFPRTLSIIHPKAYSKLAKHIHDNWEEIRFIKENENSMIKPDMHADGRIIIMNYEDAETKTIRELNDGFGRRFKVNADISGCFTNIYSHSIPWAVIGVNNAKIALNTKVKNQDKHWSDKLDYFQRQAKRNETHGVPIGPATSSIVCEIILSAVDKRLRDDGFLFRRYIDDYTCYCKTHDDAKEFLHLLGMELSKYKLSLNLHKTKITNLPGTLNDNWVSLLNVNSPTKKRFTDQDLNKLSSSEVINFLDYAVQLNTQVGGGSILKYAISLVINNLDEYTITQVYDYLLNLSWHYPMLIPYLGVLIEHVYLDDGDEYKNKFNEILSMCAENKCSDGMAWTLYFCIKNNIDIDDDVIEKIICFGDCLSLCLLDSSDIYEEKINNFVSDIIKLDYEYDIDRYWLLFYQRFFKDKAPSPYNDKCFDIMKGYGVDFMPDENYKTKAESYCHVVNNPFLEDGDEIVSFNDYMAIA

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 polymer

description	;DNA (5'-D(PCPCPCPAP*A)-3') ;
formula_weight	1449.0 kDa
src_method	man
entity_count	6

Polymer

type	polydeoxyribonucleotide
strand_id	I,C,E,G,J,L

CCCAA

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 3 non-polymer

description	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
formula_weight	467.2 kDa
src_method	syn
entity_count	6

Entity 4 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 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	2.930 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.93 Å
resolution_method	—
num_particles	277716

fit	/app/data/saxs_computation/vd/9vdo/9vdo.fit
pddf	/app/data/pr_computation/vd/9vdo/9vdo.pr.out
profile	/app/data/saxs_computation/vd/9vdo/9vdo.dat

Cryo-EM structure of the substrate bound DRT4

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)