SAXSdb — 9qlh

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1. Structure Basics

entry_id	9qlh
deposition_date	2025-03-21
title	YerA41 family-A DNA polymerase in complex with a DNA duplex
keywords	DNA replication, family-A DNA polymerase, glycosylase, DNA BINDING PROTEIN; DNA BINDING 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	39.61 Å
rg_electron	39.20 Å
i0	442220000.00
molecular_weight	164130.0 kDa
excluded_volume	202360 Å³
envelope_volume	307390 Å³
shell_volume	64441 Å³
envelope_diameter	130.4 Å
shell_rg	45.97 Å
envelope_rg	38.20 Å
shape_rg	39.18 Å
total_rg	39.68 Å
total_atoms	11516
n_residues	1311
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	124.7 Å
rg_real	39.40 Å
rg_real_error	0.79 Å
i0_real	4.4220e+08
i0_real_error	7.4840e+06
rg_reciprocal	39.54 Å
i0_reciprocal	442300000.0000
total_estimate	0.8983
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.9 Å
skewness	0.170
kurtosis	-0.479
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	37600000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.890

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	DNA polymerase
formula_weight	152801.8 kDa
ec_number	2.7.7.7
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	11516

MSTVLIGYVNIRPGKGGKLINQDVWKYFEKYVPAHFEDVDLLLFNPQTLPNLSDMIEDLNKYDNIIVTGREPLKYLGLEDAEIDRHSQFSNDDLADDQEEEEEVEDTDNEEDDDSEDDESGEESDGDDDDDDEFKVKKTKKSDNKIEVMRYFGLINNNPALKFNKIHVMYSLMMYIAKDKINVFHFDLLNRTGKNNLVPPMVQIDPKFHHISELESIYHSKWQPDEHKGFAFATRNFPFEPRFRLLGFSLANDTYQAYFYFSRDDDKYAQEMEQYRSVMVKIFLEDAKKLHTYNNKFENNAVLDQLRERIFFEDSRIYTQMLKTRGSLKFSANLFLGVPVWNEGINTFMKNYKEFVAWMKDYRELSMIEESVIDKNAYEITSIKDLLSSDDKSTLIKLLGLTETDKVKDRSRLEFKLTDDGDKKEPTYKLTTYVVETYFDLLLDPIKFVEKAMEHSQKYEQSFFKFFMTYQDRLEGKFKLTNLLTYFIKNYNEWQSCGIGDMGYYCILDGYYTVKLKEMLYDTNYDGCADGYIYYLYQSHFASLLEANKVHIDKSRFVDWMKWAYETRMYHAKKVALHPKVVENYSKSLYKKKFSGVIKTNIESVIKSYNGNKRVVAAELSFVIKYQGKDLEEMIKTYYEHLAVGRKALVDHINETGNAKLTKTQKGKIIGKEFTNDDKIIHKFIEIIDKKYKLAFFGTNPPIADRIAVISQFINHLYNRAEGMVNITYEDVKQEYLDRVNSSTDYYDIDRYLEFSSTRHEARLRMTNAVIPAGHEMVILQFLLVNRLKSTSIDHEFIDKMPSDEFGEYLVDLVKRGNLAEAGQGKRLSAADKIILLEVKTAKGTLSKILSGEKLGKHALRTIKQAWDFKNGRKNSLDEYPDFIQLIYHLQLLKRHNKSISTVIEGSLGGGSFIVSHKDSHIPIGPKTSWKDIENLPEDTQIFYKTTYWQNDKDTLRWSSSFHTIPSTLDYSLCFTPRKEGRMFFHMDMAQAEVRIAFAVAKEMGLINAILKGLDIHGFNANNAFDLGFAEDELYKIKQDPELDQLRSYAKMLTFAILYGASVGSIAKQIKKPFDEAKKIYDGYFNANPNFKKFVEDNIAELSENFGFRYLPIFNHRFYIGNPYHYSIKQKGLNYIIQNLSSSLTAYTAYALYDDLRTNYGVEIQLLGFVHDAIEFEFDAKDLFIILDRMNYWYKEMPLEKWDIPSDFDFELGSSRYSGGSCKVKYNDDKSMADIKLEIKDYYNDKEDILKLMKESFNIIEDSLKKEDHPVEKHPFVFMIDGVKPDCRFREEVTDQYVYSAKIGLK

Source

organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;
ncbi_taxonomy_id	866768
host_organism	Yersinia phage YerA41

Entity 2 polymer

description	DNA (25-MER)
formula_weight	8913.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	P

CACAGACGTAGCAGCTGGAACCTCCGTAG

Entity 3 polymer

description	DNA (29-MER)
formula_weight	11920.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

AAAATCCCCCCTACGGAGGTTCCAGCTGCTACGTCTGTG

Entity 4 non-polymer

description	2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
formula_weight	491.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

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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	5.00 Å
resolution_method	—
num_particles	30217

fit	/app/data/saxs_computation/ql/9qlh/9qlh.fit
pddf	/app/data/pr_computation/ql/9qlh/9qlh.pr.out
profile	/app/data/saxs_computation/ql/9qlh/9qlh.dat

YerA41 family-A DNA polymerase in complex with a DNA duplex

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)