SAXSdb — 9qhs

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1. Structure Basics

entry_id	9qhs
deposition_date	2025-03-16
last_revision	2026-03-25
title	phiLo family-A DNA polymerase with modified template
keywords	family-A DNA polymerase, glyscosylase, 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	39.44 Å
rg_electron	38.49 Å
i0	381936000.00
molecular_weight	148600.0 kDa
excluded_volume	181610 Å³
envelope_volume	265670 Å³
shell_volume	57214 Å³
envelope_diameter	136.7 Å
shell_rg	44.66 Å
envelope_rg	38.12 Å
shape_rg	38.45 Å
total_rg	38.99 Å
total_atoms	10414
n_residues	1186
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	130.8 Å
rg_real	39.37 Å
rg_real_error	0.88 Å
i0_real	3.8190e+08
i0_real_error	6.8300e+06
rg_reciprocal	39.42 Å
i0_reciprocal	382000000.0000
total_estimate	0.6605
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	49.0 Å
skewness	0.284
kurtosis	-0.348
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0001
highest_alpha	40050000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.999; Smooth: 0.875

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Putative DNA-directed DNA polymerase I
formula_weight	130874.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10414

HSVGYEFYGEPPYEYLLVGEAPGNDEISWGRPFIGKSGQLLRQALSEVGISSYILTNVSMCIPVVPGSKVAPPPKEAASYCSSSYLVPFIQRVRPKKVVLLGRTAIEFVLKALLGERFKEGGISDYKKTYFGVEVDGIHYFPLNHPSFVLRRGGVESQEYKTFVGELQSVVEFSHVQVEIPSDPVSFSHLFSTGKIPVSPKGRLNYHVFDLDSYEEGFSLIDDLDEVSFDVETSKGETSVDRDLVLVGLGNHEVQVAFDLREGSEENAPRFLQRLREYLDKPGRKVIVYNQSFEAGVYLQLYGEFRSFVDVFSMTKAFGLQTELYQKIGLKKTASVIFGVPEWKDRVLDYVRLAEDMSENLEDWREYLLVSPHSLKQTKIKKIESLLEKLGFDVEEAKRIFSFVLSQPGNPLIGWATVPKEVLARYNAEDVRWTHELYLFYTSLYPWEVWEVYQKQEELGSLMHQVRIRYDVEAAKRLRGEFSRIAVESFREMISSPRLTKEAIEGRLRNLKVRDVPELKEALSLAYRVHLRAYKEATKDESIVEKYKKAYQKLLSSPVLSPESEPADLSHLVVSKRESLLNSLRERLREEFERDLSMYGKENGEAWVSRMAAWFNPSSSKAYVSVFHKAISCMPLIAANYIAEVLVKRVPKEDLSLLEEELGPINTWPYKWEEVASKIFGEDWRARIYPTMLQMWESIASGLNDEYMEYLYSLFKDYLGEDLNDYPACLERVPKELAESAKLLVSFRMYKKALKVITAYLEGKNGLESVSPSREILWRGIPIPISDSEGDKHYYRTDFFVNSADTKRWRSAFHTIPTGTDLREVYISRWEEEGLWVHFDYSQMELRVLAAISGDENMLDAFKQGLDLHRYVASRIYRIPMEEVSSHQRKIAKGASFSLVYGQTPSGFAMEYTGGDVSEAQRIFDSFFQSFPRVKDYINLYRSMARTYGHVPTIFGDWIDVQRDKPDWERRAQNYPIQSSSSSVAALAGYEISMEALRLGYLAVPLAFTHDALDFDVHAKYLLSFLEIVYRLAREVPMRYGIFADIEVEVGTSFYGGLALHPEGEEDGRKVFGISGKKSVFERVLKRLEKFYEVEVLELSEGEETIPLADIFAPKKALSTLIGKTVPTVSGKIALREVSDES

Source

organism	Thermus phage phiLo
ncbi_taxonomy_id	2301536
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

description	DNA template
formula_weight	10693.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

UCCCCGCTACGGAGGTTCCAGCTGCTACGTCTGTG

Entity 3 polymer

description	DNA primer
formula_weight	9346.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	P

CACAGACGTAGCAGCTGGAACCTCCGTAGC

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	;2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE ;
formula_weight	451.2 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	3.800 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.80 Å
resolution_method	—
num_particles	70200

fit	/app/data/saxs_computation/qh/9qhs/9qhs.fit
pddf	/app/data/pr_computation/qh/9qhs/9qhs.pr.out
profile	/app/data/saxs_computation/qh/9qhs/9qhs.dat

phiLo family-A DNA polymerase with modified template

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Refinement

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)