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9r7o

DhhP of Borrelia burgdorferi in complex with AMP

Method: X-RAY DIFFRACTION D_max: 191.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r7o
deposition_date	2025-05-15
title	DhhP of Borrelia burgdorferi in complex with AMP
keywords	phosphodiesterase, c-di-AMP, cyclic di-AMP, heterobimetallic, HYDROLASE; HYDROLASE
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	54.22 Å
rg_electron	54.38 Å
i0	1130760000.00
molecular_weight	292230.0 kDa
excluded_volume	370130 Å³
envelope_volume	529180 Å³
shell_volume	85477 Å³
envelope_diameter	200.2 Å
shell_rg	53.92 Å
envelope_rg	52.49 Å
shape_rg	54.39 Å
total_rg	54.34 Å
total_atoms	20539
n_residues	2574
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	191.1 Å
rg_real	54.36 Å
rg_real_error	2.42 Å
i0_real	1.1310e+09
i0_real_error	2.5740e+07
rg_reciprocal	54.11 Å
i0_reciprocal	1130000000.0000
total_estimate	0.8577
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	65.9 Å
skewness	0.422
kurtosis	-0.099
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	50920000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.726

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	DHH family
formula_weight	36659.1 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	20549

GAMGSMRDVINFIKKYNNFVIIGHKDPDFDCIGSSLALSSFLSRIGKNSILLNEGPFIRKEIVPFKDKFLSEWPNIEISEYSVIILDCSILDRIGDEFIFYVKNMPTLVIDHHMSGEKLECEGYIDPFAPSTTFLIEKLIREFGYDLTKEEAWYILVGFCTDTGFFKFISRSDPEPFEMVARLVSKGISLKEVYSYIETTKSLKSIETLKLMLNSLESYWNGKVLFTFLSSSSSGKDGGVSGVNELFYMILSNVENNEILGILKEMEDGSIIVGLRSKDSFDVGKLAEDFGGGGHKNASGFRIKQGSLEIVKNRMLAYIKDNIYL

Source

organism	Borreliella burgdorferi
common_name	Lyme disease spirochete
ncbi_taxonomy_id	139
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	10

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6. Citations (1)

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length_a	74.745 Å
length_b	80.239 Å
length_c	132.703 Å
angle_alpha	91.24 °
angle_beta	91.30 °
angle_gamma	92.71 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.280 Å
resolution_low	40.060 Å
r_factor	0.2276
r_work	0.2263
r_free	0.2525

fit	/app/data/saxs_computation/r7/9r7o/9r7o.fit
pddf	/app/data/pr_computation/r7/9r7o/9r7o.pr.out
profile	/app/data/saxs_computation/r7/9r7o/9r7o.dat