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9q1y

Nucleotide-free structure of PmtCD in detergent LMNG

Method: ELECTRON MICROSCOPY D_max: 129.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q1y
deposition_date	2025-08-14
last_revision	2025-11-26
title	Nucleotide-free structure of PmtCD in detergent LMNG
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	37.63 Å
rg_electron	37.15 Å
i0	191540000.00
molecular_weight	122320.0 kDa
excluded_volume	157940 Å³
envelope_volume	221980 Å³
shell_volume	51029 Å³
envelope_diameter	136.7 Å
shell_rg	41.99 Å
envelope_rg	36.83 Å
shape_rg	37.21 Å
total_rg	37.32 Å
total_atoms	8632
n_residues	1074
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	129.7 Å
rg_real	37.78 Å
rg_real_error	1.58 Å
i0_real	1.9150e+08
i0_real_error	3.3410e+06
rg_reciprocal	37.69 Å
i0_reciprocal	191500000.0000
total_estimate	0.8606
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	43.2 Å
skewness	0.494
kurtosis	-0.023
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	28160000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.791; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.818

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

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

Polymer

type	polypeptide(L)
strand_id	C,D
atom_count	8632

MKLEHITKKYGSNVVLNDIDFDFGDSRIVGLIGKNGVGKTTVMKVMNGNIIKFDGKVDIDNADNIGFLIEHPKLYDNKSGLYNLKLFAQVLGKGFDKAYTDKIIDAFGMRPYIKKKVKKYSMGMKQKLAIAVSLMNKPKFLILDEPTNGMDPDGSIDVLTTIKSLVNELDMRILISSHKLEDIELICDRAVFLRDGHFVQDVNMEEGVASDTTIVTVDHKDFDRTEKYLAEHFQLQNVDKADGHLMINAQKNYQVILKALSELDIYPKYIETRKSSLRDTYFNINQRGDK

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Staphylococcus aureus

Entity 2 polymer

description	Phenol-soluble modulin export ABC transporter permease subunit PmtD
formula_weight	28220.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B

SHRILNLVKYDLYSIFKSPLTYLAILVVSSLIATQSILMANSMDNPKHIIVYGSVFAAAKWLLLIIGLMFVVKTITRDFSQGTIQLYMSKVKTRVGYIISKTISIILISILFALIHYVILIVVQASSNGKNLAFSKYVDNLWFFLIFLLFFGLFLFLITLASQKTAMIFSLGVFLVLIVPFIKPFITFIPRYGEKVLDAFDYIPFAYLTDKMISSNFDFSNWQWVISLGSIVIFFILNILYVAKKDI

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	3.80 Å
resolution_method	—
num_particles	143119

fit	/app/data/saxs_computation/q1/9q1y/9q1y.fit
pddf	/app/data/pr_computation/q1/9q1y/9q1y.pr.out
profile	/app/data/saxs_computation/q1/9q1y/9q1y.dat

Nucleotide-free structure of PmtCD in detergent LMNG

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)