SAXSdb — 9t97

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1. Structure Basics

entry_id	9t97
deposition_date	2025-11-14
title	cryo-EM structure of AccA3/AccD4/AccD5/AccE5 complex from Mycobacterium smegmatis
keywords	Bio-dependent acyl-CoA carboxylase, long chain/short chain acyl-CoA carboxylase, TRANSFERASE; TRANSFERASE
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	64.74 Å
rg_electron	64.05 Å
i0	5038170000.00
molecular_weight	599240.0 kDa
excluded_volume	750000 Å³
envelope_volume	1215800 Å³
shell_volume	151540 Å³
envelope_diameter	208.4 Å
shell_rg	70.77 Å
envelope_rg	62.60 Å
shape_rg	64.07 Å
total_rg	64.10 Å
total_atoms	42207
n_residues	5563
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	211.9 Å
rg_real	64.37 Å
rg_real_error	1.74 Å
i0_real	5.0380e+09
i0_real_error	1.0770e+08
rg_reciprocal	65.01 Å
i0_reciprocal	5044000000.0000
total_estimate	0.8874
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	88.3 Å
skewness	0.071
kurtosis	-0.676
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0001
highest_alpha	757100000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.844

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
formula_weight	63215.2 kDa
ec_number	6.3.4.14
src_method	nat
entity_count	7

Polymer

type	polypeptide(L)
strand_id	A3a,A3b,A3c,A3d,A3f,A3g,A3i
atom_count	42207

MANHASSKISKVLVANRGEIAVRVIRAAKDAGLASVAVYAEPDADAPHVRLADEAFALGGQTSAESYLVFEKILDAAEKSGANAIHPGYGFLSENADFAQAVIDAGLIWIGPSPQSIRDLGDKVTARHIAARAKAPLVPGTPDPVKDADEVVAFAKEHGVPVAIKAAFGGGGRGMKVARTLEEIPELFESATREAIAAFGRGECFVERYLDKPRHVEAQVIADQHGNVVVAGTRDCSLQRRFQKLVEEAPAPFLTDAQRKEIHESAKRICKEAGYYGAGTVEYLVGQDGLISFLEVNTRLQVEHPVTEETSGIDLVRQQFKIANGEPLDITEDPTPRGHSFEFRINGEDAGRGFLPAPGPVTKFVAPTGPGVRMDSGVETGSVIGGQFDSMLAKLIVTGATREEALERSRRALAEFTVEGLATVIPFHRAVVSDPAFIGDGEKFDVHTRWIETEWNNTVEPFTGGDPIEEEDTVPRQTVVVEVGGRRLEVSLPGDLAIGGGGGAAAPGVVRKKPKPRKRGGGGAKAASGDAVTAPMQGTVVKVAVEEGQEVSAGDLVVVLEAMKMENPVTAHKDGTITGLAVEAGAAITQGTVIAEIK

Entity 2 polymer

description	Propionyl-CoA carboxylase beta chain
formula_weight	56234.1 kDa
ec_number	6.4.1.3
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D4a,D4b

MTNKTTAELLAELREKLELAKEPGGEKAVAKREKKGIPSARARINALLDPGSFIEIGALAKTPGDPNALYGDGVVTGRGTIDGRPVGVFSHDQTVFQGSVGEMFGRKVARLMEWVAMVGCPIIGINDSAGARIQDAVTSLAWYAELGRRHEMLRGLVPEISLIFGKCAGGAVYSPIQTDLLVAVRDQGYMFITGPDVIKDVTGEDVTFDELGGADEQAKRGNIHKVVNSEAEAYQYVRDYLSFLPSNHFDNPPIVNPGMEPEITPHDLELDSIVPDADNMAYDMHEILLRIFDDGDVFEIAEQRGPAMITAFARVDGHPVGVIANQPMVLSGAIDNEASDKAASFIRFCDSYNLPLVFVVDTPGAMPGVAEEKGGIIKRGGRFFNAIVEADVPKVTVIIRKAYGGGYAVMGSKQLSADLNFAWPTARIAVIGAEGAAQLLVKRFPDPNAPEVQKIRDDFIEGYNLNMATPWIAAERGYIDAVIQPHETRLLLRKSLRLLRDKQNGPKVQRKHGLLPL

Entity 3 polymer

description	Propionyl-CoA carboxylase beta chain
formula_weight	58488.1 kDa
ec_number	6.4.1.3
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	D5a,D5b,D5c,D5d

MTSVTEPSAEHQVDIHTTAGKLADLKRRTEETLHPVGEAAVDKVHAKGKLTARERILALLDEGSFVELDALAKHRSTNFGLEKNRPLGDGVITGYGTIDGRDVCIFSQDATVFGGSLGEVYGEKIVKVQELAIKTGRPLIGINDGAGARIQEGVVSLGLYSRIFHNNIKASGVIPQISLIMGAAAGGHVYSPALTDFVVMVDQTSQMFITGPDVIKTVTGEDVTMEELGGAHTHMAKSGTAHYVASGEQDAFDYVRDLLSYLPPNNYADPPLYPVAIPEGSIEETLTDEDLELDTLIPDSPNQPYDMHEVITRILDDDEFLEVQAGYAGNIVVGFGRVEGRPVGIVANQPTQFAGCLDINASEKAARFIRTCDCFNIPIVLLVDVPGFLPGTDQEYNGIIRRGAKLLYAYGEATVAKVTVITRKSYGGAYCVMGSKDMGADVVVAWPTAQIAVMGASGAVGFVYRQQLKEAAKNGEDVDALRLELQQTYEDTLVNPYIAAERGYVDAVIPPSHTRGYVANALRLLERKIVQMPPKKHGNIPL

Entity 4 polymer

description	Acetyl-/propionyl-coenzyme A carboxylase AccE5
formula_weight	10357.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E5a,E5b

MSGANDSTTVSGEVQADVTDEAKADHEAHIKVLRGEPTPEEMAALMAVLASAGGGPAEPVKKERNMWGHPVDKLRYSVFSWQRVTLLERTHMRR

Entity 5 non-polymer

description	5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
formula_weight	228.3 kDa
src_method	syn
entity_count	5

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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	2.350 Å
resolution_low	184.960 Å
r_factor	—
r_work	0.3438
r_free	—

resolution	2.35 Å
resolution_method	—
num_particles	251974

fit	/app/data/saxs_computation/t9/9t97/9t97.fit
pddf	/app/data/pr_computation/t9/9t97/9t97.pr.out
profile	/app/data/saxs_computation/t9/9t97/9t97.dat

cryo-EM structure of AccA3/AccD4/AccD5/AccE5 complex from Mycobacterium smegmatis

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 (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)