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9q0n

;Cryo-EM structure of PPAT-NUDT5 complex bound to 6-methylthioinosine-5'-monophosphate (6-meTIMP) ;

Method: ELECTRON MICROSCOPY D_max: 148.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q0n
deposition_date	2025-08-13
title	;Cryo-EM structure of PPAT-NUDT5 complex bound to 6-methylthioinosine-5'-monophosphate (6-meTIMP) ;
keywords	Purine synthesis, phosphoribosyltransferase, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC 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	45.09 Å
rg_electron	44.51 Å
i0	2773670000.00
molecular_weight	288890.0 kDa
excluded_volume	278370 Å³
envelope_volume	533620 Å³
shell_volume	95351 Å³
envelope_diameter	160.6 Å
shell_rg	53.33 Å
envelope_rg	43.59 Å
shape_rg	44.51 Å
total_rg	44.76 Å
total_atoms	21772
n_residues	2780
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	148.9 Å
rg_real	44.81 Å
rg_real_error	1.03 Å
i0_real	2.7740e+09
i0_real_error	4.4760e+07
rg_reciprocal	45.09 Å
i0_reciprocal	2775000000.0000
total_estimate	0.8549
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	63.8 Å
skewness	0.146
kurtosis	-0.164
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	418400000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.732; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.928

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Amidophosphoribosyltransferase
formula_weight	60690.3 kDa
ec_number	2.4.2.14
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	21772

CGVFGCIASGEWPTQLDVPHVITLGLVGLQHRGQESAGIVTSDGSSVPTFKSHKGMGLVNHVFTEDNLKKLYVSNLGIGHTRYATTGKCELENCQPFVVETLHGKIAVAHNGELVNAARLRKKLLRHGIGLSTSSDSEMITQLLAYTPPQEQDDTPDWVARIKNLMKEAPTAYSLLIMHRDVIYAVRDPYGNRPLCIGRLIPVSDINDKEKKTSETEGWVVSSESCSFLSIGARYYREVLPGEIVEISRHNVQTLDIISRSEGNPVAFCIFEYVYFARPDSMFEDQMVYTVRYRCGQQLAIEAPVDADLVSTVPESATPAALAYAGKCGLPYVEVLCKNRYVGRTFIQPNMRLRQLGVAKKFGVLSDNFKGKRIVLVDDSIVRGNTISPIIKLLKESGAKEVHIRVASPPIKYPCFMGINIPTKEELIANKPEFDHLAEYLGANSVVYLSVEGLVSSVQEGIKFKKQKEKKHDIMIQENGNGLECFEKSGHCTACLTGKYPVELEWGGSKPIPNPLLGLDSTSAWSHPQFEKGGGSGGGSGGGAWSHPQFEK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	ADP-sugar pyrophosphatase
formula_weight	24523.7 kDa
ec_number	3.6.1.13,3.6.1.58,2.7.7.96
mutation	Y74F
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	E,F,G,H

GGGSGESQEPTESSQNGKQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGVAVIPVLQRTLHFECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELEEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGDGEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHANAKPFEVPFLKF

Source

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

Entity 3 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	6-(methylsulfanyl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine
formula_weight	378.3 kDa
src_method	syn
entity_count	4

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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	2.80 Å
resolution_method	—
num_particles	967122

fit	/app/data/saxs_computation/q0/9q0n/9q0n.fit
pddf	/app/data/pr_computation/q0/9q0n/9q0n.pr.out
profile	/app/data/saxs_computation/q0/9q0n/9q0n.dat

;Cryo-EM structure of PPAT-NUDT5 complex bound to 6-methylthioinosine-5'-monophosphate (6-meTIMP) ;

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 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)