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9yx0

Structure of the 3-methylcrotonyl-coenzyme A carboxylase from Mycobacterium smegmatis

Method: ELECTRON MICROSCOPY D_max: 203.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yx0
deposition_date	2025-10-26
title	Structure of the 3-methylcrotonyl-coenzyme A carboxylase from Mycobacterium smegmatis
keywords	Carboxylase, transferase, leucine catabolism, metabolism, 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	62.44 Å
rg_electron	62.27 Å
i0	6421950000.00
molecular_weight	671600.0 kDa
excluded_volume	838680 Å³
envelope_volume	1201500 Å³
shell_volume	158850 Å³
envelope_diameter	221.8 Å
shell_rg	66.28 Å
envelope_rg	61.88 Å
shape_rg	62.31 Å
total_rg	62.23 Å
total_atoms	47381
n_residues	6588
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	203.4 Å
rg_real	62.61 Å
rg_real_error	1.28 Å
i0_real	6.4200e+09
i0_real_error	1.2210e+08
rg_reciprocal	62.28 Å
i0_reciprocal	6418000000.0000
total_estimate	0.5972
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	73.2 Å
skewness	0.566
kurtosis	0.219
angular_range	— – 0.1250 Å⁻¹
current_alpha	0.0025
highest_alpha	522100000.0000
n_real_points	26
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.790; Stabil: 1.000; Sysdev: 0.004; Positv: 1.000; Valcen: 0.964; Smooth: 0.413

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Carboxyl transferase domain protein
formula_weight	54816.2 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	G,H,I,J,K,L
atom_count	47381

MSSHRDEHLALVAELRSKLAAAALGGPERARERHVGRGKLLPRDRVDGLLDPGSPFLELAPLAAGGMYDDECPGAGMIAGIGRVSGRECVIVANDATVKGGTYYPITVKKHLRAQEIALQNKLPCIYLVDSGGAFLPRQDEVFPDRDHFGRIFYNQATMSAQGIAQIAAVLGSCTAGGAYVPAMSDEAVIVRNQGTIFLGGPPLVKAATGEVVTAEELGGGDLHSKTSGVTDHLAHDDRDALRIVRNIVATLGPAEPPPWQVLPAVDPIADQTELYDVVPVDARVPYDVHEVITRIVDGGEFGEFKAEYGTTLVTGFARIHGHPVGIIANNGVLFGESAVKGAHFIELCDKRKTPLLFLQNISGFMVGRDYEAGGIAKHGAKMVTAVACARVPKLTVVIGGSYGAGNYSMCGRAYSPRFLWMWPNARISVMGGEQAASVLATVRGEMTDAEAEEFKAPIREQYEHQGNPYYSTARLWDDGVIDPADTRTVVGLALSVVGQAPLEPVSYGVFRM

Entity 2 polymer

description	biotin carboxylase
formula_weight	70144.7 kDa
ec_number	6.3.4.14
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	D,B,C,A,F,E

MMMSSQTFDTVLVANRGEIAVRVIRTLRAMGIRSVAVFSEADAGARHVTEADVAVCIGPAAARHSYLDIDAVVGAARRTDAQAVHPGYGFLSENAEFASALATAGIVFIGPPASAIATMGDKIAAKAAVSAFGVPVVPGISRPGLADDDLIAGAAEVGYPVLVKPSAGGGGKGMRVVEAAADLPAALVSARREAGAAFGDDTLFLERFVQRPRHIEVQVLADGHGNVIHLGERECSLQRRHQKVIEEAPSPLLDEATRARIGAAACATARSVDYTGAGTVEFIVSADRPDEFFFMEMNTRLQVEHPVTELVTGIDLVEQQIRIAAGEPLAIGQDDITLTGHAVEARVYAEDPAAGFLPTGGDVLGLREPTGRGVRVDSGLAAGTVVGSDYDPMLSKIIAHGSDRASALQILDRALADTAVLGVTTNIEFLRFLLADDDVAAGRLDTGLLDRRAPDFAPATVGDEQLIAAAAYLWARQWSAAGGDLWRVPSGWRVGEWAPATFRLHAGDRTDHVYITGNPERASAAVEHGDTHTVSADFTPGSDTFAVTLDGLRTDYRVAVTDSQIWLSGGGRTWSVQKVREEPVRPDDAHSGDAELVSPMPGSVVAVGVPDGSDVTAGTVVVTVEAMKMEHALTAPVDGVAKILVAVGDQVKVGQPLARITAHTQENES

Entity 3 non-polymer

description	BIOTIN
formula_weight	244.3 kDa
src_method	syn
entity_count	6

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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	2.000 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.00 Å
resolution_method	—
num_particles	30234

fit	/app/data/saxs_computation/yx/9yx0/9yx0.fit
pddf	/app/data/pr_computation/yx/9yx0/9yx0.pr.out
profile	/app/data/saxs_computation/yx/9yx0/9yx0.dat

Structure of the 3-methylcrotonyl-coenzyme A carboxylase 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 (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)