SAXSdb — 9wmi

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1. Structure Basics

entry_id	9wmi
deposition_date	2025-09-03
title	PsdAB dimer(LMNG)
keywords	ABC transpoter, TRANSPORT PROTEIN; TRANSPORT 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	40.49 Å
rg_electron	39.80 Å
i0	582246000.00
molecular_weight	210560.0 kDa
excluded_volume	269380 Å³
envelope_volume	366530 Å³
shell_volume	74431 Å³
envelope_diameter	125.3 Å
shell_rg	47.44 Å
envelope_rg	38.85 Å
shape_rg	39.79 Å
total_rg	40.28 Å
total_atoms	14823
n_residues	1861
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	124.1 Å
rg_real	40.29 Å
rg_real_error	0.66 Å
i0_real	5.8220e+08
i0_real_error	9.9140e+06
rg_reciprocal	40.49 Å
i0_reciprocal	582400000.0000
total_estimate	0.9027
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	50.9 Å
skewness	0.074
kurtosis	-0.622
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0001
highest_alpha	70100000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.907

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Lantibiotic ABC transporter ATP-binding protein PsdA
formula_weight	29073.2 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	14823

MNVLQTTNLSKTYYSNKGTISYQALSAFDLSVSKGEFVGIMGPSGSGKTTLLNLLATIDKPTQGEMMINGIQPKTLKDQELALFRRRELGFVFQDFNLLDTLTIRENILLPLALDKVKLREMEARLDELADTLQIKHILDHRTYEVSGGQQQRAACARAIIHNPALILADEPTGNLDSKSAKQVMNTLAQLNEEKEATILLVTHDATAASFCKRIVFIKDGRFFSEIHRGTNRQVFYQSILDTLSVLGGDFHEFENYRP

Source

organism	Bacillus sp. TSA-4
ncbi_taxonomy_id	3078804
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

description	Lantibiotic ABC transporter permease PsdB
formula_weight	73589.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,F

MNLRTIARKNILGNLQRYVAYFLSCVFAVSVFFVFTSFIFHPDVNEDNIYGGSLVKTCLSAALVVIIVFCIFFITYSNSAFLQARKKEFGLLTLFGTSKQQLRKMIYYEQSLISLAAIAAGIGAGLLFSKLFFMIMTWMLSVKVPISFAIVPKAFVMTIAGFLILFQTLLILSLGRIRKLEIIELIKSAKKPKSLPVYSKWLTVLSLLCLGSGYYLSATANAIDMMFRVFPILILVLVGTYFFFTQSSVAFFRMLYRKKHSFYKGTNIIVRSNMIFRLKDHARMLFLTSVITAVILTATGVIYMFYSDLQRQEEQSIPQSVSWVEKDASRFQVMKPETAENTLKKAHAVIKYKVDATGIPVTFQSDLPYGNKKMEAEALLISEKVYNQVAKEKGFPVIHLQENEAFINVSFQMMVKDTFGEGETAAFHMKSGKTLSYVMKKQQNKGILMSVDGVSRLLVVSEKSFDSLSQDVPLKEQMRMVGYELEHWQETVDVSEKLENMVPKEHTSDFQTRAPSYQIVKQGVALMLFIGLFVSVLFFIVQGSMLYLRMFTEIEDTRVQVLALKRIGVTDKEIHSILGKQIGFLFFIPFIAGTIHAGFAYAALSNMLNSNLFLEAVIVIFIYFVFQALYYIVTRHIYKRAVLQRM

Source

organism	Bacillus sp. TSA-4
ncbi_taxonomy_id	3078804
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 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	3.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.90 Å
resolution_method	—
num_particles	61164

fit	/app/data/saxs_computation/wm/9wmi/9wmi.fit
pddf	/app/data/pr_computation/wm/9wmi/9wmi.pr.out
profile	/app/data/saxs_computation/wm/9wmi/9wmi.dat

PsdAB dimer(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

Refinement

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)