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9yx5

Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with MSMEG_0435-MSMEG_0436 bound

Method: ELECTRON MICROSCOPY D_max: 258.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yx5
deposition_date	2025-10-26
title	Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with MSMEG_0435-MSMEG_0436 bound
keywords	Carboxylase, transferase, lipid synthesis, mycolic acid synthesis, LIGASE; LIGASE
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	70.86 Å
rg_electron	70.21 Å
i0	18768700000.00
molecular_weight	743270.0 kDa
excluded_volume	705920 Å³
envelope_volume	1698400 Å³
shell_volume	194250 Å³
envelope_diameter	241.7 Å
shell_rg	72.91 Å
envelope_rg	71.09 Å
shape_rg	70.19 Å
total_rg	70.27 Å
total_atoms	56321
n_residues	8786
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	258.6 Å
rg_real	74.31 Å
rg_real_error	1.78 Å
i0_real	1.8870e+10
i0_real_error	4.1790e+08
rg_reciprocal	70.95 Å
i0_reciprocal	18770000000.0000
total_estimate	0.6328
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	94.0 Å
skewness	0.585
kurtosis	0.289
angular_range	— – 0.1100 Å⁻¹
current_alpha	0.8775
highest_alpha	852800000.0000
n_real_points	23
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.680; Stabil: 0.881; Sysdev: 0.006; Positv: 1.000; Valcen: 0.968; Smooth: 0.651

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4. Crystallography & Experiment

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5. Entities & Polymer Info (12)

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	14

Polymer

type	polypeptide(L)
strand_id	A,I,J,K,L,Q,X,U,B,C,D,R,S,T
atom_count	56321

MANHASSKISKVLVANRGEIAVRVIRAAKDAGLASVAVYAEPDADAPHVRLADEAFALGGQTSAESYLVFEKILDAAEKSGANAIHPGYGFLSENADFAQAVIDAGLIWIGPSPQSIRDLGDKVTARHIAARAKAPLVPGTPDPVKDADEVVAFAKEHGVPVAIKAAFGGGGRGMKVARTLEEIPELFESATREAIAAFGRGECFVERYLDKPRHVEAQVIADQHGNVVVAGTRDCSLQRRFQKLVEEAPAPFLTDAQRKEIHESAKRICKEAGYYGAGTVEYLVGQDGLISFLEVNTRLQVEHPVTEETSGIDLVRQQFKIANGEPLDITEDPTPRGHSFEFRINGEDAGRGFLPAPGPVTKFVAPTGPGVRMDSGVETGSVIGGQFDSMLAKLIVTGATREEALERSRRALAEFTVEGLATVIPFHRAVVSDPAFIGDGEKFDVHTRWIETEWNNTVEPFTGGDPIEEEDTVPRQTVVVEVGGRRLEVSLPGDLAIGGGGGAAAPGVVRKKPKPRKRGGGGAKAASGDAVTAPMQGTVVKVAVEEGQEVSAGDLVVVLEAMKMENPVTAHKDGTITGLAVEAGAAITQGTVIAEIK

Entity 2 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	E,P

MSGANDSTTVSGEVQADVTDEAKADHEAHIKVLRGEPTPEEMAALMAVLASAGGGPAEPVKKERNMWGHPVDKLRYSVFSWQRVTLLERTHMRR

Entity 3 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	F,O

MTNKTTAELLAELREKLELAKEPGGEKAVAKREKKGIPSARARINALLDPGSFIEIGALAKTPGDPNALYGDGVVTGRGTIDGRPVGVFSHDQTVFQGSVGEMFGRKVARLMEWVAMVGCPIIGINDSAGARIQDAVTSLAWYAELGRRHEMLRGLVPEISLIFGKCAGGAVYSPIQTDLLVAVRDQGYMFITGPDVIKDVTGEDVTFDELGGADEQAKRGNIHKVVNSEAEAYQYVRDYLSFLPSNHFDNPPIVNPGMEPEITPHDLELDSIVPDADNMAYDMHEILLRIFDDGDVFEIAEQRGPAMITAFARVDGHPVGVIANQPMVLSGAIDNEASDKAASFIRFCDSYNLPLVFVVDTPGAMPGVAEEKGGIIKRGGRFFNAIVEADVPKVTVIIRKAYGGGYAVMGSKQLSADLNFAWPTARIAVIGAEGAAQLLVKRFPDPNAPEVQKIRDDFIEGYNLNMATPWIAAERGYIDAVIQPHETRLLLRKSLRLLRDKQNGPKVQRKHGLLPL

Entity 4 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	G,H,M,N

MTSVTEPSAEHQVDIHTTAGKLADLKRRTEETLHPVGEAAVDKVHAKGKLTARERILALLDEGSFVELDALAKHRSTNFGLEKNRPLGDGVITGYGTIDGRDVCIFSQDATVFGGSLGEVYGEKIVKVQELAIKTGRPLIGINDGAGARIQEGVVSLGLYSRIFHNNIKASGVIPQISLIMGAAAGGHVYSPALTDFVVMVDQTSQMFITGPDVIKTVTGEDVTMEELGGAHTHMAKSGTAHYVASGEQDAFDYVRDLLSYLPPNNYADPPLYPVAIPEGSIEETLTDEDLELDTLIPDSPNQPYDMHEVITRILDDDEFLEVQAGYAGNIVVGFGRVEGRPVGIVANQPTQFAGCLDINASEKAARFIRTCDCFNIPIVLLVDVPGFLPGTDQEYNGIIRRGAKLLYAYGEATVAKVTVITRKSYGGAYCVMGSKDMGADVVVAWPTAQIAVMGASGAVGFVYRQQLKEAAKNGEDVDALRLELQQTYEDTLVNPYIAAERGYVDAVIPPSHTRGYVANALRLLERKIVQMPPKKHGNIPL

Entity 5 polymer

description	Allophanate hydrolase subunit 2
formula_weight	31280.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	V,Y

MGTTLEVLRTGPLALVEDLGRPGLAHMGVTRSGAADRRSHTLANRLVANPGESATIEVTFGGFSARVCGGDVAIAVTGADTDPAVNGIPFGTNSIHHVHDGQVISLGAPHSGLRSYLAVRGGIDVTPVLGSRSYDVMSAIGPSPLRPGDVLPVGEHTDEFPELDQAPVAAIAEDVVELQVVPGPRDDWFVDPDILVRTNWLVTNRSDRVGMRLVGMPLEYRNPDRQLPSEGATRGAIQVPPNGFPVILGPDHPVTGGYPVIGVVTEEDIDKLGQVRPGQTVRLHWAYPRRPFET

Entity 6 polymer

description	Allophanate hydrolase subunit 1
formula_weight	22659.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	W,Z

MTLGTVHNYGDQALLLEFDSTAEVLAWTETLREAELLGVVDIVPAARTVLVKLAGPRYQAPTRQRLGKLRVRPEAITHQPPGDRVDVTIDVVYDGADLHEVASLTGMTPAQVIAAHTGTPWRVGFCGFAPGFAYLVDGDARLQVPRRAEPRTSVPAGAVALAGEFSGVYPRQSPGGWQLIGHTDAVMFDVNRDKPALLTPGMWVQFRAVG

Entity 7 non-polymer

description	;S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (11E,14E,16E)-icosa-11,14,16-trienethioate (non-preferred name) ;
formula_weight	1056.0 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	propionyl Coenzyme A
formula_weight	823.6 kDa
src_method	syn
entity_count	4

Entity 9 non-polymer

description	BIOTIN
formula_weight	244.3 kDa
src_method	syn
entity_count	5

Entity 10 non-polymer

description	BICARBONATE ION
formula_weight	61.0 kDa
src_method	syn
entity_count	2

Entity 11 non-polymer

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

Entity 12 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

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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	2.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.90 Å
resolution_method	—
num_particles	10016

fit	/app/data/saxs_computation/yx/9yx5/9yx5.fit
pddf	/app/data/pr_computation/yx/9yx5/9yx5.pr.out
profile	/app/data/saxs_computation/yx/9yx5/9yx5.dat

Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with MSMEG_0435-MSMEG_0436 bound

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 (12)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)