SAXSdb — 9qrl

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1. Structure Basics

entry_id	9qrl
deposition_date	2025-04-03
title	DNA polymerase with inhibitor #2
keywords	DNA polymerase, inhibitor complex, 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	35.98 Å
rg_electron	35.98 Å
i0	518952000.00
molecular_weight	121540.0 kDa
excluded_volume	116450 Å³
envelope_volume	208970 Å³
shell_volume	48593 Å³
envelope_diameter	125.3 Å
shell_rg	42.23 Å
envelope_rg	35.62 Å
shape_rg	35.99 Å
total_rg	36.25 Å
total_atoms	9159
n_residues	1117
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	117.3 Å
rg_real	36.02 Å
rg_real_error	0.97 Å
i0_real	5.1900e+08
i0_real_error	8.6110e+06
rg_reciprocal	36.00 Å
i0_reciprocal	518900000.0000
total_estimate	0.6617
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	40.0 Å
skewness	0.359
kurtosis	-0.410
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	47840000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 0.028; Positv: 1.000; Valcen: 0.984; Smooth: 0.796

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	DNA polymerase III PolC-type
formula_weight	166595.8 kDa
ec_number	2.7.7.7
mutation	D431A, E433A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9160

MGSSHHHHHHSSGLVPRGSHMHMSEKRDLFEKLLEQIQLEEAEKNHPLLTAGEMDSVVVHRKSRLWEFTLHFSKILPIMLYRSLTQHLTIAFKDIAQVKLNILADDQTFDEQLLQDYWAQALENQQCDTPLAQQVLKTQVPVIKDRKVILPIDSTGAISYLKQQYLPLVEELFVSYGFPKFRIEPEVDEQQAERVLKLFEERKQEQAEAFMKQAAESLVVHEQKKKERKEQSPALEGPIHIQLGRNIPADEPTTPMISIVEEERRVTLEGYVFDKEVRELRSKRKILTLKITDYTSSFIVKKFSNGEKDEQVFDAISVGSWLKVRGSIQEDTFVRDLVMNAQDIIEVKHTPRKDYAPEGEKRVELHVHSNMSTMDATNSISDLVAQAGKWGHRAIAITDHGGAQAFPEAHSAGKKAGVKILYGVEANVVDDGVPIAYNDAHEALSEATYVVFAVATTGLSAVYDTIIELAAVKMYKGNVIESFDEFIDPGHPLSRTTVDLTGITDGMVRGSKSEEEVLRMFLEFSKDTILVAHNAAFDMGFLNTSYARYGIPEAANPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLEQHHRAIYDAEATGHLAWIFVKEAMDNHNMLYHDQLNEHIGEGDSYKRARPFHVTILAKNQAGLKDLFKLISMSNVEYFERVPRIPRSQLKKMRENLLIGSACDKGEIFEAMMQKGVEEARNRAKFYDYIEVMPKAVYAPLIEQELVKNEHDLEEIIQNLVEIGKSLDKIVVATGNVHYLNEEDAIYRKILINSMGGANPLNRHSLPDVHFRTTDEMLTAFHFLGEETAKEIVVENTNKIADICEEVIPVKDELYTPKIPGSEDEISELSYTKAKQMYGDPLPEIIQKRLKKELNSINGNGFSVIYLIAQKLVHKSNEDGYLVGSRGSVGSSFVATMTGITEVNPLAPHYYCPECQYSEFFEDGTYGSGFDMPEKQCPKCGARLNKDGHDIPFETFLGFHGDKVPDIDLNFSGDYQAEAHNYTKVLFGEDYVYRAGTIGTVADKTAYGYVKGYERDNNLQFRSAEVDRLAKGATGVKRTTGQHPGGIIVIPDYMDVYDFTPIQYPADDQNSEWKTTHFDFHSIHDNVLKLDILGHDDPTVIRMLQDLSGIDPQTIPTDDPEVMRIFAGPEVLGVSQEQIYSKTGTLGIPEFGTRFVRGMLEETHPTTFAELLQISGLSHGTDVWLGNAEELIRRGDATLAEVIGCRDDIMVYLIHAGLDSGMAFKIMETVRKGQWNKIPDELRETYLSAMKENNVPDWYIDSCSKIKYMFPKAHAAAYVLMALRVAYFKVYFPILYYCAYFSVRADDFDLVSMCKGKDAVKQAMKEITDKGLDASVKEKNQLTVLELANEMLERGFKFGMIDLYKSDAVNFVIEGDTLIAPFRAVPSLGTNVAKQIVEARKDGPFLSKEDLATRGKVSKTLIEYMNDNGVLKDLPDENQLSLFDML

Source

organism	Enterococcus faecium
ncbi_taxonomy_id	1352
host_organism	Escherichia coli

Entity 2 polymer

description	;DNA (5'-D(PTPAP*A)-3') ;
formula_weight	885.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E

TAA

Entity 3 polymer

description	;DNA (5'-D(PGPGPTPGPCPGPCPAP*T)-3') ;
formula_weight	10179.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	P

TAGGACGAAGGACTCCCAACTTTAGGTGCGCAT

Entity 4 polymer

description	;DNA (5'-D(PCPCPAPTPGPCPGPCPAPCP*C)-3') ;
formula_weight	12724.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

CCCCCCCCCATGCGCACCTAAAGTTGGGAGTCCTTCGTCCTA

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	Ibezapolstat
formula_weight	423.3 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
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	3.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.20 Å
resolution_method	—
num_particles	330001

fit	/app/data/saxs_computation/qr/9qrl/9qrl.fit
pddf	/app/data/pr_computation/qr/9qrl/9qrl.pr.out
profile	/app/data/saxs_computation/qr/9qrl/9qrl.dat

DNA polymerase with inhibitor #2

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

EM 3D

5. Entities & Polymer Info (8)

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 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)