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9y19

WT human DNA polymerase beta, Ternary complex dA:dUmpNpp

Method: X-RAY DIFFRACTION D_max: 73.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y19
deposition_date	2025-08-29
title	WT human DNA polymerase beta, Ternary complex dA:dUmpNpp
keywords	polymerase, REPLICATION, HYDROLASE-DNA complex; REPLICATION, HYDROLASE/DNA
method	X-RAY DIFFRACTION

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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	22.94 Å
rg_electron	22.26 Å
i0	48285400.00
molecular_weight	47229.0 kDa
excluded_volume	56286 Å³
envelope_volume	70900 Å³
shell_volume	26070 Å³
envelope_diameter	75.3 Å
shell_rg	29.53 Å
envelope_rg	22.40 Å
shape_rg	22.26 Å
total_rg	23.06 Å
total_atoms	3278
n_residues	357
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	73.1 Å
rg_real	22.80 Å
rg_real_error	0.43 Å
i0_real	4.8290e+07
i0_real_error	7.1190e+05
rg_reciprocal	22.83 Å
i0_reciprocal	48290000.0000
total_estimate	0.8943
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.4 Å
skewness	0.140
kurtosis	-0.424
angular_range	— – 0.3450 Å⁻¹
current_alpha	0.0000
highest_alpha	5764000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	DNA polymerase beta
formula_weight	38241.7 kDa
ec_number	2.7.7.7,4.2.99.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3801

MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Template strand
formula_weight	4853.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

CCGACAGCGCATCAGC

Entity 3 polymer

description	Primer strand
formula_weight	3061.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	P

GCTGATGCGC

Entity 4 polymer

description	Downstream
formula_weight	1536.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

GTCGG

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE ;
formula_weight	467.2 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	505

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6. Citations (1)

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length_a	50.678 Å
length_b	79.275 Å
length_c	55.497 Å
angle_alpha	90.00 °
angle_beta	107.24 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.900 Å
resolution_low	24.990 Å
r_factor	0.1528
r_work	0.1479
r_free	0.1971

fit	/app/data/saxs_computation/y1/9y19/9y19.fit
pddf	/app/data/pr_computation/y1/9y19/9y19.pr.out
profile	/app/data/saxs_computation/y1/9y19/9y19.dat

WT human DNA polymerase beta, Ternary complex dA:dUmpNpp

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

Diffraction

5. Entities & Polymer Info (9)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)