SAXSdb — 9whk

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1. Structure Basics

entry_id	9whk
deposition_date	2025-08-27
title	Structure of Klebsiella pneumoniae trypsin-HamAB bound with DNA, dimer
keywords	ATPase, Helicase, DNA BINDING PROTEIN/DNA, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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	47.53 Å
rg_electron	47.17 Å
i0	989787000.00
molecular_weight	267740.0 kDa
excluded_volume	337250 Å³
envelope_volume	438120 Å³
shell_volume	75958 Å³
envelope_diameter	167.0 Å
shell_rg	52.76 Å
envelope_rg	46.63 Å
shape_rg	47.15 Å
total_rg	47.42 Å
total_atoms	18888
n_residues	2286
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	155.6 Å
rg_real	47.44 Å
rg_real_error	1.54 Å
i0_real	9.8980e+08
i0_real_error	1.9570e+07
rg_reciprocal	47.53 Å
i0_reciprocal	989900000.0000
total_estimate	0.8943
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	51.9 Å
skewness	0.188
kurtosis	-0.638
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	170100000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.875

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
formula_weight	59614.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	18888

MSIDIADKLGVKISYNNKNSSGFICHGDDYSYVLTAKHSICKSSPNDCKFKHKKCDTCVFSGVAKNKVSICKPDTDTFPLCKVKDVLLSPKKDVAILVLNKKSHIDLKTKELPSTKIINTANYNSSHKFVSCGYPAINEHQSVQPLHYNNFSLFRNEKICLQIINDTLTALEDPKNGLSGNSGAGIILNSSSCVGLLGLYTDTGDYGICYGDIVDFSINELLTSSGYVPLEMEEDLSNNFKALIQSDFMECFVRMECDLNLDKNRIVNLYRLCLDGKKYNYVKIGERLIDCIPSFSLSRKQLMRCRERNAFGKATLSAIRNFLKIERKTKISEMLLQGFLESYLHAPKLYSFDEINNAGFHGAHVKFNKNRNVELIHSAAFISNSLSDGVSYAIDVILKAFPELRSLDGLLGNTFLETNFTEDECQILASLLIPGESSYSQGYEDRLAIFIGYNHKIEESLIYENASRFPSLLEQKIILNVQQALEYRKEEINKLSIVNATIDCFFVPFDDVNKFNDEFIESLKNEED

Source

organism	Klebsiella pneumoniae
ncbi_taxonomy_id	573
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	DNA polymerase theta (Helicase domain only)
formula_weight	99035.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

MKKIDSFIIEKIFNSAYFKKLYKKIIKAYSALTIESENHFNISNTELRDIFRFIDLLANSSNQNARMCAYHWISLLEPFSDKWGKFSLISSLVYSKLGLYALDFNDHALPFSQRLENEAKKSAQTFSNTYIFTDAQFDIYTDMLKSPYYSFSGPTSLGKSFILKRYIEEIIQNSTSNIVILVPTRALISQFSLEIKNELHELIENFNYKIVTHGSLASKSDAVIIKHIFILTPERLLNLFSQGKVVSIDYLFVDEAHKLSNNDDSDVRSLTEYNAIDSALFNNPNMKIVFSSPNIENPEVFLNLFGREKIYASRIIESPVSQNLYLIDFHKKEIKYFSNSECIDIESGSLYTLNKKSDFIYNIGSRHGSNMIYCSSRAKAVDSALEFYQIRLSENIVLSPLLIDSIKKISNYIHPEYYLAMFLMKRIAYHHGQLPQAIRNIVEELFRKGDIDFIFCTPTLVEGVNMPTRNIFINCDDKIRLIADAKKNPNKTLAFWNLAGRAGRYCKELSGNIFCLQDESNRWDNTDIFLEKTAHLTTTIDARIESKSGLREIERYLSDTETDIYKRNQAIEYLANIMAVDTIRFKNNLKDSFVLRKFYDIHREELLSLAKLKANDILDIPIDIINSYKSLNFKIQRKVFDYVSVSPVNKKLPSLDYANILSVLELFYDLYRWGETETKYVKSKGQLTYFATLMNQWTNDYSINRIINENIDIKRTIVIERGQQPIPFDKNDINHVNKVIDDILYNIERILSFFFEKYFNHYYKCLAAILGEDNAGHNWATFLEYGSKNPLCISLQTLGISRHAANIIASSKELRKYLKFNEDSYEIISVNKQGLLNSLQKDSVEYGEVKIFL

Source

organism	Klebsiella pneumoniae
ncbi_taxonomy_id	573
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	;DNA (5'-D(PAPAPAPAPAPAPAPAP*A)-3') ;
formula_weight	2773.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

AAAAAAAAA

Entity 4 polymer

description	;DNA (5'-D(PAPAPAPAPAPAP*A)-3') ;
formula_weight	2147.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	F

AAAAAAA

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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	3.22 Å
resolution_method	—
num_particles	88815

fit	/app/data/saxs_computation/wh/9whk/9whk.fit
pddf	/app/data/pr_computation/wh/9whk/9whk.pr.out
profile	/app/data/saxs_computation/wh/9whk/9whk.dat

Structure of Klebsiella pneumoniae trypsin-HamAB bound with DNA, dimer

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)