SAXSdb — 9xdc

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1. Structure Basics

entry_id	9xdc
deposition_date	2025-10-27
title	TamAB hybrid barrel state
keywords	;outer membrane, interaction, hybrid, TamAB, PROTEIN TRANSPORT, TamA, TamB, lipid transport, outer membrane insertion, 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	41.34 Å
rg_electron	41.55 Å
i0	142541000.00
molecular_weight	95704.0 kDa
excluded_volume	119530 Å³
envelope_volume	193270 Å³
shell_volume	41104 Å³
envelope_diameter	159.3 Å
shell_rg	43.71 Å
envelope_rg	41.56 Å
shape_rg	41.56 Å
total_rg	41.65 Å
total_atoms	6763
n_residues	888
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	148.9 Å
rg_real	41.78 Å
rg_real_error	1.69 Å
i0_real	1.4250e+08
i0_real_error	2.5560e+06
rg_reciprocal	41.35 Å
i0_reciprocal	142500000.0000
total_estimate	0.8156
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	39.2 Å
skewness	0.618
kurtosis	-0.025
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	12240000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.717; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.794; Smooth: 0.656

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Translocation and assembly module subunit TamA
formula_weight	64843.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6763

VRYIRQLCCVSLLCLSGSAVAANVRLQVEGLSGQLEKNVRAQLSTIESDEVTPDRRFRARVDDAIREGLKALGYYQPTIEFDLRPPPKKGRQVLIAKVTPGVPVLIGGTDVVLRGGARTDKDYLKLLDTRPAIGTVLNQGDYENFKKSLTSIALRKGYFDSEFTKAQLGIALGLHKAFWDIDYNSGERYRFGHVTFEGSQIRDEYLQNLVPFKEGDEYESKDLAELNRRLSATGWFNSVVVAPQFDKARETKVLPLTGVVSPRTENTIETGVGYSTDVGPRVKATWKKPWMNSYGHSLTTSTSISAPEQTLDFSYKMPLLKNPLEQYYLVQGGFKRTDLNDTESDSTTLVASRYWDLSSGWQRAINLRWSLDHFTQGEITNTTMLFYPGVMISRTRSRGGLMPTWGDSQRYSIDYSNTAWGSDVDFSVFQAQNVWIRTLYDRHRFVTRGTLGWIETGDFDKVPPDLRFFAGGDRSIRGYKYKSIAPKYANGDLKGASKLITGSLEYQYNVTGKWWGAVFVDSGEAVSDIRRSDFKTGTGVGVRWESPVGPIKLDFAVPVADKDEHGLQFYIGLGPEL

Source

organism	Escherichia coli str. K-12 substr. MG1655star
ncbi_taxonomy_id	879462
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Translocation and assembly module subunit TamB
formula_weight	136905.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MSLWKKISLGVVIVILLLLGSVAFLVGTTSGLHLVFKAADRWVPGLDIGKVTGGWRDLTLSDVRYEQPGVAVKAGNLHLAVGLECLWNSSVCINDLALKDIQVNIDSKKMPPSEQVEEEEDSGPLDLSTPYPITLTRVALDNVNIKIDDTTVSVMDFTSGLNWQEKTLTLKPTSLKGLLIALPKVAEVAQEEVVEPKIENPQPDEKPLGETLKDLFSRPVLPEMTDVHLPLNLNIEEFKGEQLRVTGDTDITVSTMLLKVSSIDGNTKLDALDIDSSQGIVNASGTAQLSDNWPVDITLNSTLNVEPLKGEKVKLKMGGALREQLEIGVNLSGPVDMDLRAQTRLAEAGLPLNVEVNSKQLYWPFTGEKQYQADDLKLKLTGKMTDYTLSMRTAVKGQEIPPATITLDAKGNEQQVNLDKLTVAALEGKTELKALLDWQQAISWRGELTLNGINTAKEFPDWPSKLNGLIKTRGSLYGGTWQMDVPELKLTGNVKQNKVNVDGTLKGNSYMQWMIPGLHLELGPNSAEVKGELGVKDLNLDATINAPGLDNALPGLGGTAKGLVKVRGTVEAPQLLADITARGLRWQELSVAQVRVEGDIKSTDQIAGKLDVRVEQISQPDVNINLVTLNAKGSEKQHELQLRIQGEPVSGQLNLAGSFDRKEERWKGTLSNTRFQTPVGPWSLTRDIALDYRNKEQKISIGPHCWLNPNAELCVPQTIDAGAEGRAVVNLNRFDLAMLKPFMPETTQASGIFTGKADVAWDTTKEGLPQGSITLSGRNVQVTQTVNDAALPVAFQTLNLTAELRNNRAELGWTIRLTNNGQFDGQVQVTDPQGRRNLGGNVNIRNFNLAMINPIFTRGEKAAGMVSANLRLGGDVQSPQLFGQLQVTGVDIDGNFMPFDMQPSQLAVNFNGMRSTLAGTVRTQQGEIYLNGDADWSQIENWRARVTAKGSKVRITVPPMVRMDVSPDVVFEATPNLFTLDGRVDVPWARIVVHDLPESAVGVSSDVVMLNDNLQPEEPKTASIPINSNLIVHVGNNVRIDAFGLKARLTGDLNVVQDKQGLGLNGQINIPEGRFHAYGQDLIVRKGELLFSGPPDQPYLNIEAIRNPDATEDDVIAGVRVTGLADEPKAEIFSDPAMSQQAALSYLLRGQGLESDQSDSAAMTSMLIGLGVAQSGQIVGKIGETFGVSNLALDTQGVGDSSQVVVSGYVLPGLQVKYGVGIFDSIATLTLRYRLMPKLYLEAVSGVDQALDLLYQFEF

Source

organism	Escherichia coli str. K-12 substr. MG1655star
ncbi_taxonomy_id	879462
host_organism	Escherichia coli BL21(DE3)

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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	3.690 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.69 Å
resolution_method	—
num_particles	110602

fit	/app/data/saxs_computation/xd/9xdc/9xdc.fit
pddf	/app/data/pr_computation/xd/9xdc/9xdc.pr.out
profile	/app/data/saxs_computation/xd/9xdc/9xdc.dat

TamAB hybrid barrel state

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)