SAXSdb — 9qli

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1. Structure Basics

entry_id	9qli
deposition_date	2025-03-21
title	YerA41 family-A DNA polymerase
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	40.57 Å
rg_electron	39.98 Å
i0	305705000.00
molecular_weight	146470.0 kDa
excluded_volume	185240 Å³
envelope_volume	289770 Å³
shell_volume	60358 Å³
envelope_diameter	137.7 Å
shell_rg	46.18 Å
envelope_rg	38.69 Å
shape_rg	39.95 Å
total_rg	40.52 Å
total_atoms	10352
n_residues	1257
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	129.7 Å
rg_real	40.43 Å
rg_real_error	0.93 Å
i0_real	3.0570e+08
i0_real_error	5.4520e+06
rg_reciprocal	40.57 Å
i0_reciprocal	305700000.0000
total_estimate	0.8985
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	53.2 Å
skewness	0.145
kurtosis	-0.485
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	32700000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.913

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

Entity 1 polymer

description	DNA polymerase
formula_weight	152888.9 kDa
ec_number	2.7.7.7
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10352

MSTVLIGYVNIRPGKGGKLINQDVWKYFEKYVPAHFEDVDLLLFNPQTLPNLSDMIEDLNKYDNIIVTGREPLKYLGLEDAEIDRHSQFSNDDLADDQEEEEEVEDTDNEEDDDSEDDESGEESDGDDDDDDEFKVKKTKKSDNKIEVMRYFGLINNNPALKFNKIHVMYSLMMYIAKDKINVFHFDLLVRTGKNNLVPPMVQIDPKFHHISELESIYHSKWQPDEHKGFDFETRNFPFEPRFRLLGFSLANDTYQAYFYFSRDDDKYAQEMEQYRSVMVKIFLEDAKKLHTYNNKFENNAVLDQLRERIFFEDSRIYTQMLKTRGSLKFSANLFLGVPVWNEGINTFMKNYKEFVAWMKDYRELSMIEESVIDKNAYEITSIKDLLSSDDKSTLIKLLGLTETDKVKDRSRLEFKLTDDGDKKEPTYKLTTYVVETYFDLLLDPIKFVEKAMEHSQKYEQSFFKFFMTYQDRLEGKFKLTNLLTYFIKNYNEWQSCGIGDMGYYCILDGYYTVKLKEMLYDTNYDGCADGYIYYLYQSHFASLLEANKVHIDKSRFVDWMKWAYETRMYHAKKVALHPKVVENYSKSLYKKKFSGVIKTNIESVIKSYNGNKRVVAAELSFVIKYQGKDLEEMIKTYYEHLAVGRKALVDHINETGNAKLTKTQKGKIIGKEFTNDDKIIHKFIEIIDKKYKLAFFGTNPPIADRIAVISQFINHLYNRAEGMVNITYEDVKQEYLDRVNSSTDYYDIDRYLEFSSTRHEARLRMTNAVIPAGHEMVILQFLLVNRLKSTSIDHEFIDKMPSDEFGEYLVDLVKRGNLAEAGQGKRLSAADKIILLEVKTAKGTLSKILSGEKLGKHALRTIKQAWDFKNGRKNSLDEYPDFIQLIYHLQLLKRHNKSISTVIEGSLGGGSFIVSHKDSHIPIGPKTSWKDIENLPEDTQIFYKTTYWQNDKDTLRWSSSFHTIPSTLDYSLCFTPRKEGRMFFHMDMAQAEVRIAFAVAKEMGLINAILKGLDIHGFNANNAFDLGFAEDELYKIKQDPELDQLRSYAKMLTFAILYGASVGSIAKQIKKPFDEAKKIYDGYFNANPNFKKFVEDNIAELSENFGFRYLPIFNHRFYIGNPYHYSIKQKGLNYIIQNLSSSLTAYTAYALYDDLRTNYGVEIQLLGFVHDAIEFEFDAKDLFIILDRMNYWYKEMPLEKWDIPSDFDFELGSSRYSGGSCKVKYNDDKSMADIKLEIKDYYNDKEDILKLMKESFNIIEDSLKKEDHPVEKHPFVFMIDGVKPDCRFREEVTDQYVYSAKIGLK

Source

organism	Yersinia phage YerA41
ncbi_taxonomy_id	2815754
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

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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	50000

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

YerA41 family-A DNA polymerase

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 (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)