SAXSdb — 1dxy

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1. Structure Basics

entry_id	1dxy
deposition_date	1996-08-13
title	STRUCTURE OF D-2-HYDROXYISOCAPROATE DEHYDROGENASE
keywords	D-2-HYDROXYCARBOXYLATE DEHYDROGENASE, D-LACTATE DEHYDROGENASE, OXIDOREDUCTASE; OXIDOREDUCTASE
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	22.87 Å
rg_electron	22.05 Å
i0	23523600.00
molecular_weight	37455.0 kDa
excluded_volume	46977 Å³
envelope_volume	55667 Å³
shell_volume	21525 Å³
envelope_diameter	78.2 Å
shell_rg	28.33 Å
envelope_rg	22.16 Å
shape_rg	22.05 Å
total_rg	22.86 Å
total_atoms	2638
n_residues	330
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	78.0 Å
rg_real	22.86 Å
rg_real_error	0.47 Å
i0_real	2.3520e+07
i0_real_error	3.1100e+05
rg_reciprocal	22.86 Å
i0_reciprocal	23520000.0000
total_estimate	0.8816
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.0 Å
skewness	0.316
kurtosis	-0.441
angular_range	— – 0.3450 Å⁻¹
current_alpha	0.0000
highest_alpha	4322000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	D-2-HYDROXYISOCAPROATE DEHYDROGENASE
formula_weight	36929.8 kDa
ec_number	1.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2833

MKIIAYGARVDEIQYFKQWAKDTGNTLEYHTEFLDENTVEWAKGFDGINSLQTTPYAAGVFEKMHAYGIKFLTIRNVGTDNIDMTAMKQYGIRLSNVPAYSPAAIAEFALTDTLYLLRNMGKVQAQLQAGDYEKAGTFIGKELGQQTVGVMGTGHIGQVAIKLFKGFGAKVIAYDPYPMKGDHPDFDYVSLEDLFKQSDVIDLHVPGIEQNTHIINEAAFNLMKPGAIVINTARPNLIDTQAMLSNLKSGKLAGVGIDTYEYETEDLLNLAKHGSFKDPLWDELLGMPNVVLSPHIAYYTETAVHNMVYFSLQHLVDFLTKGETSTEVTGPAK

Source

organism	Lactobacillus casei
ncbi_taxonomy_id	1582
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	2-OXO-4-METHYLPENTANOIC ACID
formula_weight	130.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	182

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6. Citations (7)

;Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution. ;

J.Mol.Biol. (1997)

PMID: 9126843 · DOI: 10.1006/jmbi.1996.0864 PRIMARY

Crystallization and Preliminary Characterization of Crystals of D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei

J.Mol.Biol. (1994)

;Roentgenkristallographische Untersuchungen an Drei Mikrobiellen Enzymen: D-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus Casei L-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus Confusus Alkalische Protease Aus Bacillus Alcalophilus/Variante Q59R ;

Thesis (1993)

Potential of R-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei for Stereospecific Reductions

ENZYME.MICROB.TECHNOL. (1992)

Cloning, Sequencing and Expression in Escherichia Coli of the D-2-Hydroxyisocaproate Dehydrogenase Gene of Lactobacillus Casei

Gene (1989)

Crystallization and Molecular Properties of D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei

Fems Microbiol.Lett. (1987)

;D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei. A New Enzyme Suitable for Stereospecific Reduction of 2-Ketocarboxylic Acids ;

Appl.Microbiol.Biotechnol. (1985)

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length_a	134.100 Å
length_b	134.100 Å
length_c	125.100 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 63 2 2
int_tables_number	182
crystal_system	—

resolution	1.860 Å
resolution_low	12.100 Å
r_factor	0.1960
r_work	0.1960
r_free	0.2170

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

STRUCTURE OF D-2-HYDROXYISOCAPROATE DEHYDROGENASE

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