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9q2r

ADP-bound structure of PmtCD in peptidisc

Method: ELECTRON MICROSCOPY D_max: 125.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q2r
deposition_date	2025-08-15
last_revision	2025-11-26
title	ADP-bound 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	36.46 Å
rg_electron	36.02 Å
i0	200640000.00
molecular_weight	124000.0 kDa
excluded_volume	159690 Å³
envelope_volume	216560 Å³
shell_volume	51224 Å³
envelope_diameter	134.8 Å
shell_rg	41.14 Å
envelope_rg	36.02 Å
shape_rg	36.07 Å
total_rg	36.21 Å
total_atoms	8744
n_residues	1082
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	125.7 Å
rg_real	36.64 Å
rg_real_error	1.21 Å
i0_real	2.0060e+08
i0_real_error	3.3560e+06
rg_reciprocal	36.53 Å
i0_reciprocal	200600000.0000
total_estimate	0.8405
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	40.9 Å
skewness	0.566
kurtosis	0.108
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	38180000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.683

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Phenol-soluble modulin export ABC transporter permease subunit PmtD
formula_weight	28631.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8744

VPRGSHRILNLVKYDLYSIFKSPLTYLAILVVSSLIATQSILMANSMDNPKHIIVYGSVFAAAKWLLLIIGLMFVVKTITRDFSQGTIQLYMSKVKTRVGYIISKTISIILISILFALIHYVILIVVQASSNGKNLAFSKYVDNLWFFLIFLLFFGLFLFLITLASQKTAMIFSLGVFLVLIVPFIKPFITFIPRYGEKVLDAFDYIPFAYLTDKMISSNFDFSNWQWVISLGSIVIFFILNILYVAKKDI

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

Entity 3 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	2

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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	4.20 Å
resolution_method	—
num_particles	142155

fit	/app/data/saxs_computation/q2/9q2r/9q2r.fit
pddf	/app/data/pr_computation/q2/9q2r/9q2r.pr.out
profile	/app/data/saxs_computation/q2/9q2r/9q2r.dat

ADP-bound 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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)