SAXSdb — 9qpc

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1. Structure Basics

entry_id	9qpc
deposition_date	2025-03-26
title	DNA polymerase with inhibitor
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	36.91 Å
rg_electron	36.83 Å
i0	642212000.00
molecular_weight	135130.0 kDa
excluded_volume	129240 Å³
envelope_volume	232350 Å³
shell_volume	52739 Å³
envelope_diameter	125.3 Å
shell_rg	43.16 Å
envelope_rg	36.16 Å
shape_rg	36.85 Å
total_rg	37.07 Å
total_atoms	10174
n_residues	1240
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	120.8 Å
rg_real	36.87 Å
rg_real_error	1.17 Å
i0_real	6.4220e+08
i0_real_error	1.0410e+07
rg_reciprocal	36.90 Å
i0_reciprocal	642200000.0000
total_estimate	0.8927
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.0 Å
skewness	0.288
kurtosis	-0.426
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	50330000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.885

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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	10177

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(PTPAPGPGPTPGPCPGPCPAP*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(PCPCPAPTPGPCPGPCPAPCPCPTP*A)-3') ;
formula_weight	12724.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

CCCCCCCCCATGCGCACCTAAAGTTGGGAGTCCTTCGTCCTA

Entity 5 non-polymer

description	5-[[2,2-bis(fluoranyl)-1,3-benzodioxol-5-yl]methylamino]-3-fluoranyl-1-(2-hydroxyethyl)-6~{H}-pyrazolo[4,3-d]pyrimidin-7-one
formula_weight	383.3 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	3

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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	2.800 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.80 Å
resolution_method	—
num_particles	15572

fit	/app/data/saxs_computation/qp/9qpc/9qpc.fit
pddf	/app/data/pr_computation/qp/9qpc/9qpc.pr.out
profile	/app/data/saxs_computation/qp/9qpc/9qpc.dat

DNA polymerase with inhibitor

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)