← Back to search

9ubg

Cryo-EM structure of Pyruvate carboxylase from Mycobacterium tuberculosis in complex with Acetyl-CoA and ADP

Method: ELECTRON MICROSCOPY D_max: 176.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9ubg
deposition_date	2025-04-03
title	Cryo-EM structure of Pyruvate carboxylase from Mycobacterium tuberculosis in complex with Acetyl-CoA and ADP
keywords	Pyruvate Carboxylase, Pyruvate, Acetyl CoA, Mycobacterium tuberculosis, LIGASE; LIGASE
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	60.16 Å
rg_electron	59.80 Å
i0	3006640000.00
molecular_weight	452360.0 kDa
excluded_volume	562400 Å³
envelope_volume	882160 Å³
shell_volume	119320 Å³
envelope_diameter	186.1 Å
shell_rg	66.97 Å
envelope_rg	57.07 Å
shape_rg	59.80 Å
total_rg	59.97 Å
total_atoms	33679
n_residues	4180
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	176.2 Å
rg_real	59.89 Å
rg_real_error	0.96 Å
i0_real	3.0070e+09
i0_real_error	6.0510e+07
rg_reciprocal	60.36 Å
i0_reciprocal	3009000000.0000
total_estimate	0.8424
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	88.1 Å
skewness	0.079
kurtosis	-0.556
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	380100000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.066

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	Pyruvate carboxylase
formula_weight	112527.5 kDa
ec_number	6.4.1.1
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,C,D,B
atom_count	33685

MFSKVLVANRGEIAIRAFRAAYELGVGTVAVYPYEDRNSQHRLKADESYQIGDIGHPVHAYLSVDEIVATARRAGADAIYPGYGFLSENPDLAAACAAAGISFVGPSAEVLELAGNKSRAIAAAREAGLPVLMSSAPSASVDELLSVAAGMPFPLFVKAVAGGGGRGMRRVGDIAALPEAIEAASREAESAFGDPTVYLEQAVINPRHIEVQILADNLGDVIHLYERDCSVQRRHQKVIELAPAPHLDAELRYKMCVDAVAFARHIGYSCAGTVEFLLDERGEYVFIEMNPRVQVEHTVTEEITDVDLVASQLRIAAGETLEQLGLRQEDIAPHGAALQCRITTEDPANGFRPDTGRISALRTAGGAGVRLDGSTNLGAEISPYFDSMLVKLTCRGRDLPTAVSRARRAIAEFRIRGVSTNIPFLQAVLDDPDFRAGRVTTSFIDERPQLLTARASADRGTKILNFLADVTVNNPYGSRPSTIYPDDKLPDLDLRAAPPAGSKQRLVKLGPEGFARWLRESAAVGVTDTTFRDAHQSLLATRVRTSGLSRVAPYLARTMPQLLSVECWGGATYDVALRFLKEDPWERLATLRAAMPNICLQMLLRGRNTVGYTPYPEIVTSAFVQEATATGIDIFRIFDALNNIESMRPAIDAVRETGSAIAEVAMCYTGDLTDPGEQLYTLDYYLKLAEQIVDAGAHVLAIKDMAGLLRPPAAQRLVSALRSRFDLPVHLHTHDTPGGQLASYVAAWHAGADAVDGAAAPLAGTTSQPALSSIVAAAAHTEYDTGLSLSAVCALEPYWEALRKVYAPFESGLPGPTGRVYHHEIPGGQLSNLRQQAIALGLGDRFEEIEEAYAGADRVLGRLVKVTPTSKVVGDLALALVGAGVSADEFASDPARFGIPESVLGFLRGELGDPPGGWPEPLRTAALAGRGAARPTAQLAADDEIALSSVGAKRQATLNRLLFPSPTKEFNEHREAYGDTSQLSANQFFYGLRQGEEHRVKLERGVELLIGLEAISEPDERGMRTVMCILNGQLRPVLVRDRSIA

Source

organism	Mycobacterium tuberculosis H37Rv
ncbi_taxonomy_id	83332
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	ACETYL COENZYME *A
formula_weight	809.6 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	6

▶

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	2.700 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.70 Å
resolution_method	—
num_particles	536403

fit	/app/data/saxs_computation/ub/9ubg/9ubg.fit
pddf	/app/data/pr_computation/ub/9ubg/9ubg.pr.out
profile	/app/data/saxs_computation/ub/9ubg/9ubg.dat