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9q0d

CryoEM structure of methylmalonic acid semialdehyde dehydrogenase from Burkholderia cenocepacia at 2.38A resolution

Method: ELECTRON MICROSCOPY D_max: 114.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q0d
deposition_date	2025-08-12
title	CryoEM structure of methylmalonic acid semialdehyde dehydrogenase from Burkholderia cenocepacia at 2.38A resolution
keywords	OXIDOREDUCTASE, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID; OXIDOREDUCTASE
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	37.88 Å
rg_electron	37.01 Å
i0	705685000.00
molecular_weight	214950.0 kDa
excluded_volume	268040 Å³
envelope_volume	334150 Å³
shell_volume	71183 Å³
envelope_diameter	113.8 Å
shell_rg	45.98 Å
envelope_rg	37.00 Å
shape_rg	37.01 Å
total_rg	37.51 Å
total_atoms	15128
n_residues	1988
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	114.5 Å
rg_real	37.59 Å
rg_real_error	0.52 Å
i0_real	7.0570e+08
i0_real_error	1.1600e+07
rg_reciprocal	37.77 Å
i0_reciprocal	705800000.0000
total_estimate	0.8316
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	49.1 Å
skewness	0.073
kurtosis	-0.586
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	201400000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	methylmalonate-semialdehyde dehydrogenase (CoA acylating)
formula_weight	55120.8 kDa
ec_number	1.2.1.27
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	15478

MAHHHHHHMTTVPAYTSDADVGHYLDGAPVAGRSGRFQDVFNPALGRAVRRVALAGNDEVERAVASARAAFPAWADTPPIRRARVLHRFLQLMNEHRDTLAAIITAEHGKVFSDAQGEVARGIDIIEFACGVPQLLKGDFTDQVSTGIDNWTMRQPLGVVAGITPFNFPCMVPCWMFPVALATGNTFVLKPSERDPSAALFIADLLTQAGLPAGVFNVVQGDKGAVDALLDHPDVQAVSFVGSTPIAAYVQQRAVQSGKRVQALGGAKNHLVVMPDANIDQAVDALIGAAYGSAGERCMAISIAVLVGDVADKIVPAVAERARKLVIGDGMSPEVEMGPIVTGEALKRIEGYIEQGVNEGAQLVVDGRGLRVPGREAGFFTGGTLFDHVKPDMRIYKEEIFGPVLGCVRVKDFGEAVDLINAHEFGNGVSCFTSDGGIAREFARRIQVGMVGINVPIPVPMAWHGFGGWKKSLFGDMHAYGEEGVRFYTRQKSVMQRWSSSIGKGAEFAMPTAK

Source

organism	Burkholderia cenocepacia
ncbi_taxonomy_id	95486
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	346

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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	triclinic

resolution	2.38 Å
resolution_method	—
num_particles	2412495

fit	/app/data/saxs_computation/q0/9q0d/9q0d.fit
pddf	/app/data/pr_computation/q0/9q0d/9q0d.pr.out
profile	/app/data/saxs_computation/q0/9q0d/9q0d.dat