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1dxf

2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli in complex with pyruvate

Method: X-RAY DIFFRACTION D_max: 88.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dxf
deposition_date	2000-01-05
title	2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli in complex with pyruvate
keywords	CLASS II ALDOLASE; CLASS II ALDOLASE
method	X-RAY DIFFRACTION

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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	27.84 Å
rg_electron	27.04 Å
i0	47537300.00
molecular_weight	54456.0 kDa
excluded_volume	68442 Å³
envelope_volume	80611 Å³
shell_volume	25867 Å³
envelope_diameter	86.5 Å
shell_rg	33.38 Å
envelope_rg	26.83 Å
shape_rg	27.06 Å
total_rg	27.65 Å
total_atoms	3836
n_residues	502
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	88.5 Å
rg_real	27.94 Å
rg_real_error	0.52 Å
i0_real	4.7540e+07
i0_real_error	6.9020e+05
rg_reciprocal	27.91 Å
i0_reciprocal	47540000.0000
total_estimate	0.8832
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.4 Å
skewness	0.331
kurtosis	-0.721
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	9535000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.912; Smooth: 0.951

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE
formula_weight	27504.9 kDa
ec_number	4.1.2.20
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4080

MNNDVFPNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVSHRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGHLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFRSATQKLADTFKK

Entity 2 non-polymer

description	PYRUVIC ACID
formula_weight	88.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	244

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6. Citations (1)

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length_a	126.400 Å
length_b	126.400 Å
length_c	172.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	36

space_group	H 3 2
int_tables_number	155
crystal_system	—

resolution	2.600 Å
resolution_low	20.000 Å
r_factor	0.1730
r_work	0.1730
r_free	0.2330

fit	/app/data/saxs_computation/dx/1dxf/1dxf.fit
pddf	/app/data/pr_computation/dx/1dxf/1dxf.pr.out
profile	/app/data/saxs_computation/dx/1dxf/1dxf.dat

2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli in complex with pyruvate

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

Diffraction