SAXSdb — 9tdm

▼

1. Structure Basics

entry_id	9tdm
deposition_date	2025-11-24
title	Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA
keywords	Bio-dependent acyl-CoA carboxylase, long chain/short chain acyl-CoA carboxylase, TRANSFERASE; TRANSFERASE
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	76.44 Å
rg_electron	76.40 Å
i0	9578150000.00
molecular_weight	823190.0 kDa
excluded_volume	1028400 Å³
envelope_volume	1767400 Å³
shell_volume	197220 Å³
envelope_diameter	257.0 Å
shell_rg	73.31 Å
envelope_rg	74.83 Å
shape_rg	76.46 Å
total_rg	76.17 Å
total_atoms	114486
n_residues	7618
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	215.7 Å
rg_real	74.88 Å
rg_real_error	0.81 Å
i0_real	9.4190e+09
i0_real_error	1.6190e+08
rg_reciprocal	75.85 Å
i0_reciprocal	9563000000.0000
total_estimate	0.8903
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	97.1 Å
skewness	0.395
kurtosis	-0.194
angular_range	— – 0.1000 Å⁻¹
current_alpha	0.1733
highest_alpha	417100000.0000
n_real_points	21
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.661

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

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	8

Polymer

type	polypeptide(L)
strand_id	A3a,A3b,A3c,A3d,A3e,A3f,A3g,A3h
atom_count	114486

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	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	2

Entity 6 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

Entity 7 non-polymer

description	propionyl Coenzyme A
formula_weight	823.6 kDa
src_method	syn
entity_count	4

▶

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	2.400 Å
resolution_low	380.800 Å
r_factor	—
r_work	—
r_free	—

resolution	2.40 Å
resolution_method	—
num_particles	52469

fit	/app/data/saxs_computation/td/9tdm/9tdm.fit
pddf	/app/data/pr_computation/td/9tdm/9tdm.pr.out
profile	/app/data/saxs_computation/td/9tdm/9tdm.dat

Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA

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 (7)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)