SAXSdb — 9sri

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1. Structure Basics

entry_id	9sri
deposition_date	2025-09-24
title	Human DNA polymerase epsilon bound to DNA blunt end
keywords	POLE1, DNA, polymerase, epsilon, PCNA, leading strand, replication, replisome, 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	43.81 Å
rg_electron	43.50 Å
i0	872657000.00
molecular_weight	233370.0 kDa
excluded_volume	287900 Å³
envelope_volume	440700 Å³
shell_volume	82322 Å³
envelope_diameter	141.0 Å
shell_rg	50.75 Å
envelope_rg	41.88 Å
shape_rg	43.52 Å
total_rg	43.80 Å
total_atoms	16305
n_residues	1968
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	139.2 Å
rg_real	43.60 Å
rg_real_error	0.95 Å
i0_real	8.7270e+08
i0_real_error	1.5000e+07
rg_reciprocal	43.81 Å
i0_reciprocal	872900000.0000
total_estimate	0.8977
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	54.1 Å
skewness	0.153
kurtosis	-0.527
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	125400000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.947

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	DNA polymerase epsilon catalytic subunit A
formula_weight	138137.6 kDa
ec_number	2.7.7.7,3.1.11.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	16305

MSLRSGGRRRADPGADGEASRDDGATSSVSALKRLERSQWTDKMDLRFGFERLKEPGEKTGWLINMHPTEILDEDKRLGSAVDYYFIQDDGSRFKVALPYKPYFYIATRKGCEREVSSFLSKKFQGKIAKVETVPKEDLDLPNHLVGLKRNYIRLSFHTVEDLVKVRKEISPAVKKNREQDHASDAYTALLSSVLQRGGVITDEEETSKKIADQLDNIVDMREYDVPYHIRLSIDLKIHVAHWYNVRYRGNAFPVEITRRDDLVERPDPVVLAFAIATTKLPLKFPDAETDQIMMISYMIDGQGYLITNREIVSEDIEDFEFTPKPEYEGPFCVFNEPDEAHLIQRWFEHVQETKPTIMVTYNGDFFDWPFVEARAAVHGLSMQQEIGFQKDSQGEYKAPQCIHMDCLRWVKRDSYLPVGSHNLKAAAKAKLGYDPVELDPEDMCRMATEQPQTLATYSVSDAVATYYLYMKYVHPFIFALCTIIPMEPDEVLRKGSGTLCEALLMVQAFHANIIFPNKQEQEFNKLTDDGHVLDSETYVGGHVEALESGVFRSDIPCRFRMNPAAFDFLLQRVEKTLRHALEEEEKVPVEQVTNFEEVCDEIKSKLASLKDVPSRIECPLIYHLDVGAMYPNIILTNRLQPSAMVDEATCAACDFNKPGANCQRKMAWQWRGEFMPASRSEYHRIQHQLESEKFPPLFPEGPARAFHELSREEQAKYEKRRLADYCRKAYKKIHITKVEERLTTICQRENSFYVDTVRAFRDRRYEFKGLHKVWKKKLSAAVEVGDAAEVKRCKNMEVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGRPLELDTDGIWCVLPNSFPENFVFKTTNVKKPKVTISYPGAMLNIMVKEGFTNDQYQELAEPSSLTYVTRSENSIFFEVDGPYLAMILPASKEEGKKLKKRYAVFNEDGSLAELKGFEVKRRGELQLIKIFQSSVFEAFLKGSTLEEVYGSVAKVADYWLDVLYSKAANMPDSELFELISENRSMSRKLEDYGEQKSTSISTAKRLAEFLGDQMVKDAGLSCRYIISRKPEGSPVTERAIPLAIFQAEPTVRKHFLRKWLKSSSLQDFDIRAILDWDYYIERLGSAIQKIITIPAALQQVKNPVPRVKHPDWLHKKLLEKNDVYKQKKISELFTLEGRRQVTMAEA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

description	Proliferating cell nuclear antigen
formula_weight	28795.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,C,D

MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEGS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	Primer DNA oligonucleotide
formula_weight	7090.6 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	P

CCTTCCACTTCCCAACCCTCACCA

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	synthetic construct

Entity 4 polymer

description	Template DNA oligonucleotide
formula_weight	12033.7 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

AAGGCTGAACGAATTGGTGAGGGTTGGGAAGTGGAAGG

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	synthetic construct

Entity 5 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 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	triclinic

resolution	3.30 Å
resolution_method	—
num_particles	221792

fit	/app/data/saxs_computation/sr/9sri/9sri.fit
pddf	/app/data/pr_computation/sr/9sri/9sri.pr.out
profile	/app/data/saxs_computation/sr/9sri/9sri.dat

Human DNA polymerase epsilon bound to DNA blunt end

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

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)