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9qyf

PARP9 Macro Domain 2 in complex with ADPr

Method: X-RAY DIFFRACTION D_max: 54.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qyf
deposition_date	2025-04-17
last_revision	2025-05-28
title	PARP9 Macro Domain 2 in complex with ADPr
keywords	Complex, ADP-ribose, ADPribosylation, PARP9, Macro domain, TRANSFERASE; TRANSFERASE
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	17.09 Å
rg_electron	15.90 Å
i0	8542700.00
molecular_weight	22138.0 kDa
excluded_volume	27994 Å³
envelope_volume	30880 Å³
shell_volume	16052 Å³
envelope_diameter	53.9 Å
shell_rg	22.24 Å
envelope_rg	16.29 Å
shape_rg	15.89 Å
total_rg	17.02 Å
total_atoms	1554
n_residues	190
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	54.6 Å
rg_real	16.98 Å
rg_real_error	0.29 Å
i0_real	8.5430e+06
i0_real_error	1.0650e+05
rg_reciprocal	17.00 Å
i0_reciprocal	8543000.0000
total_estimate	0.8872
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.3 Å
skewness	0.154
kurtosis	-0.343
angular_range	— – 0.4650 Å⁻¹
current_alpha	0.0000
highest_alpha	2102000.0000
n_real_points	77
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Protein mono-ADP-ribosyltransferase PARP9
formula_weight	22232.9 kDa
ec_number	2.4.2.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1863

GAMATTPSFNAMVVNNLTLQIVQGHIEWQTADVIVNSVNPHDITVGPVAKSILQQAGVEMKSEFLATKAKQFQRSQLVLVTKGFNLFCKYIYHVLWHSEFPKPQILKHAMKECLEKCIEQNITSISFPALGTGNMEIKKETAAEILFDEVLTFAKDHVKHQLTVKFVIFPTDLEIYKAFSSEMAKRSKMLSLNNYSV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ADENOSINE-5-DIPHOSPHORIBOSE
formula_weight	559.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ;
formula_weight	559.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	211

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6. Citations (1)

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length_a	52.143 Å
length_b	52.143 Å
length_c	132.158 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	1.300 Å
resolution_low	40.970 Å
r_factor	0.1352
r_work	0.1333
r_free	0.1731

fit	/app/data/saxs_computation/qy/9qyf/9qyf.fit
pddf	/app/data/pr_computation/qy/9qyf/9qyf.pr.out
profile	/app/data/saxs_computation/qy/9qyf/9qyf.dat

PARP9 Macro Domain 2 in complex with ADPr

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