SAXSdb — 9pxi

▼

1. Structure Basics

entry_id	9pxi
deposition_date	2025-08-05
title	Cryo-EM structure of BAM from P. aeruginosa PAO1 in complex with Pyocin L1
keywords	;protein complex, outer membrane, beta-barrel, protein folding, Gram-negative bacterial protein, L-type bacteriocin, pyocin, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	51.09 Å
rg_electron	51.27 Å
i0	486038000.00
molecular_weight	181260.0 kDa
excluded_volume	226520 Å³
envelope_volume	355510 Å³
shell_volume	61677 Å³
envelope_diameter	167.7 Å
shell_rg	50.78 Å
envelope_rg	49.26 Å
shape_rg	51.26 Å
total_rg	51.28 Å
total_atoms	12801
n_residues	1640
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

▼

3. P(r) Analysis (GNOM)

dmax	175.5 Å
rg_real	51.26 Å
rg_real_error	1.29 Å
i0_real	4.8620e+08
i0_real_error	9.0950e+06
rg_reciprocal	51.04 Å
i0_reciprocal	486000000.0000
total_estimate	0.6487
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	62.3 Å
skewness	0.223
kurtosis	-0.679
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0506
highest_alpha	27350000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 0.999; Sysdev: 0.000; Positv: 1.000; Valcen: 0.896; Smooth: 0.870

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	Outer membrane protein assembly factor BamD
formula_weight	38660.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D
atom_count	12801

MQVKHLLLIAILALTAACSSNKETVDENLSESQLYQQAQDDLNNKSYNSAVTKLKALESRYPFGRYAEQAQLELIYANYKNMEPEAARAAAERFIRLHPQHPNVDYAYYLKGLSSFDQDRGLLARFLPLDMTKRDPGAARDSFNEFAQLTSRFPNSRYAPDAKARMVYLRNLLAAYEVHVGHYYLKRQAYVAAANRGRYVVENFQETPAVGDGLAIMVEAYRRLGLDDLASTSLETLKLNYPDNASLKDGEFVARESEADTRSWLAKATLGLIEGGEPPPHMETQAAKDVIKQYEDAEREIPAELKPENQDHSADDEKPESDDDEDSGRSWWSYMTFGLFD

Entity 2 polymer

description	Outer membrane protein assembly factor BamC
formula_weight	43100.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MKRLAGLTALALVIGNTSGCGWLWGPEGYFRDRGDDYLGARETPPMQLPEGVHSKPLDPLLPIPLNVATTHEKEGEYEVPRPQPLANAGDISDYSLQRSGDSRWVVAQRPPAEVWPVARQFFEENGFRIADERPQTGEFSSDWQSLSQLSAPLARRLSSRVSGVEPDGQARVRVRIEPGVQSNTSEVYVLSQTRAAGDTSSPSWPSKSVAPSLDAALLDEMVASMARSAEQGGSVSLLAANSIYDTPGTFELSKDGSGNPVLTLQSDFDRSWVSVGRALDNADIRVDDLNRSLGVYYVNIAEGAKKPDEDKPGFFSRLFGGGEKTKEEEDAKAQRYQVRLTTVSDAVQVTVDKDINTSAPADVAQNVLEKLQESMRNAVRGSGQRKPGQFGLGEQF

Entity 3 polymer

description	Outer membrane protein assembly factor BamB
formula_weight	40436.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MVQWKHAALLALALAVVGCSSNSKKELPPAELTDFKEEVVLSKQWSRSVGDGQGDLYNLLEPAVDGSTIYAASAEGRVMAIQRETGDVLWKKDLERPVSGGVGVGYGLVLVGTLRGDVIALDEATGKKKWTKRVNSEVLSAPATNGDVVVVQTQDDKLIGLDAASGDQRWIYESTVPVLTLRGTGAPLIAGNMALAGLASGKVVAVDVQRGLPIWEQRVAIPQGRSELDRVVDIDGGLLLSGDTLYVVSYQGRAAALDVNSGRLLWQREASSYVGVAEGFGNIYVSQASGSVEGLDSRGASSLWNNDALARRQLSAPAVFSSNVVVGDLEGYVHLLSQVDGRFVGRERVDSDGVRVRPLVVGSWMYVFGNGGKLVAYTIR

Entity 4 polymer

description	Outer membrane protein assembly factor BamA
formula_weight	92258.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MKRFLLPALLSALMIAEVHAESAWSHPQFEKGGGSGGGSGGSAWSHPQFEKENLYFQGSFTVSDIRVNGLQRVSAGSVFAALPLNVGETIDDQALVQATRSLFKTGFFQDIQLGRDGNVLVVTVVERPSISSIEIEGNKAISKEDLLKGLKQSGLAEGEIFQRATLEGVRNELQRQYVAQGRYSAEINAEVIPQPRNRVALKININEGTVAAISHINVVGNTVFSEEDLTDLFELKTTNWLSFFKNDDKYAREKLSGDLERLRSYYLDRGYINMDIASTQVSITPDKKHVYITVNINEGEKYTIRDVKLTGDLKVPEEEVKRLLLVQKGQVFSRKVMTTTSDLITRRLGNEGYTFANVNGVPEAHDDDKTVSVTFVVDPGKRAYVNRINFRGNTKTEDEVLRREMRQMEGGWASTYLIDQSKARLERLGYFKEVNVETPAVPGTDDQVDVNYSVEEQPSGSITASVGFAQSAGLILGGSISQNNFLGTGNKVSIGLTRSEYQTRYNFGFVDPYWTVDGVSLGYNAFYRKTDYDELDVDVASYSVNSLGAGMSIGYPISETSRLTYGLSVQRDQIDTGRYTVDEIYDFLDKEGDNFTNFKASIGWSESTLNKGVLATRGHSQSLTLETTLPGSDLSFYKIDYRGQVFAPLTDNYTMRFHTELGYGDGYGSTERLPFYENYYAGGFNSVRGFKDSTLGPRSTPSVARNPDGTPMKNQGPDSKGRYTDPDQDPEAFGGNILITGGAELLFPLPFVKDQRQLRTVLFWDVGSTFDTDCPTKTTTNCDGIKTDNLASSVGVGLTWITALGPLSFSLATPIKKPDNAETQVFQFSLGQTF

Entity 5 polymer

description	Outer membrane protein assembly factor BamE
formula_weight	19411.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MQNAKLMLTCLAFAGLAALAGCSFPGVYKIDIQQGNVVTQDMIDQLRPGMTRRQVRFIMGNPLIVDTFHANRWDYLYSIQPGGGRRQQERVSLFFNDSDQLAGLNGDFMPGVSRDEAILGKEGSTTVTQPADQQKPEAQKEEPPKPGSTLEQLQREVDEAQPVPVPTPEPLDPSPQ

Entity 6 polymer

description	Pyocin L1
formula_weight	30609.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MGSSHHHHHHSSGLVPRGSHMASSLAPRQVIRDGQFITSPNGKYKLVMQADGNLVLYEDGTKPIWNTTPVGPGAKAVMEFNLNLYNKAGQVAWSSNVYTAYLFEEFKDEAYLNLQDDGDFGIFSDEAKWGSIVLSRPEVGVKNKIIPTGTVMVPGTEYINGNYRLAFQGDGNLVIYQINPQVVIWATYTMGADRAVVQEDGNFVIYKGTTALWHTHTATGMPAYLKFTNTGKLFLSQPTLLWTLKRGSLSKPPKVIPGQHGPLDTTPIWSWPHDYP

Source

organism	Pseudomonas aeruginosa
ncbi_taxonomy_id	287
host_organism	Escherichia coli BL21(DE3)

▶

6. Citations (1)

▶

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	2.85 Å
resolution_method	—
num_particles	110600

fit	/app/data/saxs_computation/px/9pxi/9pxi.fit
pddf	/app/data/pr_computation/px/9pxi/9pxi.pr.out
profile	/app/data/saxs_computation/px/9pxi/9pxi.dat

Cryo-EM structure of BAM from P. aeruginosa PAO1 in complex with Pyocin L1

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 (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)