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9q2q

Nucleotide-free structure of PmtCD in peptidisc

Method: ELECTRON MICROSCOPY D_max: 131.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q2q
deposition_date	2025-08-15
last_revision	2025-11-26
title	Nucleotide-free structure of PmtCD in peptidisc
keywords	ABC transporter, MEMBRANE PROTEIN; MEMBRANE 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	37.51 Å
rg_electron	36.97 Å
i0	193826000.00
molecular_weight	122750.0 kDa
excluded_volume	158430 Å³
envelope_volume	224090 Å³
shell_volume	51539 Å³
envelope_diameter	137.3 Å
shell_rg	42.09 Å
envelope_rg	36.64 Å
shape_rg	37.03 Å
total_rg	37.16 Å
total_atoms	8662
n_residues	1078
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	131.8 Å
rg_real	37.64 Å
rg_real_error	1.32 Å
i0_real	1.9380e+08
i0_real_error	3.5810e+06
rg_reciprocal	37.56 Å
i0_reciprocal	193800000.0000
total_estimate	0.8571
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	44.0 Å
skewness	0.493
kurtosis	-0.025
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	31020000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.889

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Phenol-soluble modulin export ABC transporter permease subunit PmtD
formula_weight	28435.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8662

RGSHRILNLVKYDLYSIFKSPLTYLAILVVSSLIATQSILMANSMDNPKHIIVYGSVFAAAKWLLLIIGLMFVVKTITRDFSQGTIQLYMSKVKTRVGYIISKTISIILISILFALIHYVILIVVQASSNGKNLAFSKYVDNLWFFLIFLLFFGLFLFLITLASQKTAMIFSLGVFLVLIVPFIKPFITFIPRYGEKVLDAFDYIPFAYLTDKMISSNFDFSNWQWVISLGSIVIFFILNILYVAKKDI

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Staphylococcus aureus

Entity 2 polymer

description	ABC transporter ATP-binding protein
formula_weight	33001.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

MKLEHITKKYGSNVVLNDIDFDFGDSRIVGLIGKNGVGKTTVMKVMNGNIIKFDGKVDIDNADNIGFLIEHPKLYDNKSGLYNLKLFAQVLGKGFDKAYTDKIIDAFGMRPYIKKKVKKYSMGMKQKLAIAVSLMNKPKFLILDEPTNGMDPDGSIDVLTTIKSLVNELDMRILISSHKLEDIELICDRAVFLRDGHFVQDVNMEEGVASDTTIVTVDHKDFDRTEKYLAEHFQLQNVDKADGHLMINAQKNYQVILKALSELDIYPKYIETRKSSLRDTYFNINQRGDK

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Staphylococcus aureus

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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	4.30 Å
resolution_method	—
num_particles	108661

fit	/app/data/saxs_computation/q2/9q2q/9q2q.fit
pddf	/app/data/pr_computation/q2/9q2q/9q2q.pr.out
profile	/app/data/saxs_computation/q2/9q2q/9q2q.dat

Nucleotide-free structure of PmtCD in peptidisc

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)