SAXSdb — 1dio

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1. Structure Basics

entry_id	1dio
deposition_date	1999-01-27
title	DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA
keywords	COENZYME B12, PROPANEDIOL, POTASSIUM ION, TIM BARREL, LYASE; LYASE
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	37.42 Å
rg_electron	37.17 Å
i0	565415000.00
molecular_weight	192680.0 kDa
excluded_volume	240340 Å³
envelope_volume	278610 Å³
shell_volume	60581 Å³
envelope_diameter	125.5 Å
shell_rg	44.81 Å
envelope_rg	37.51 Å
shape_rg	37.18 Å
total_rg	37.50 Å
total_atoms	13516
n_residues	1734
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	123.6 Å
rg_real	37.45 Å
rg_real_error	0.89 Å
i0_real	5.6540e+08
i0_real_error	8.8330e+06
rg_reciprocal	37.44 Å
i0_reciprocal	565400000.0000
total_estimate	0.8810
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.2 Å
skewness	0.377
kurtosis	-0.451
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	168700000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.920

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	PROTEIN (DIOL DEHYDRATASE)
formula_weight	60408.1 kDa
ec_number	4.2.1.28
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,L
atom_count	13912

MRSKRFEALAKRPVNQDGFVKEWIEEGFIAMESPNDPKPSIKIVNGAVTELDGKPVSDFDLIDHFIARYGINLNRAEEVMAMDSVKLANMLCDPNVKRSEIVPLTTAMTPAKIVEVVSHMNVVEMMMAMQKMRARRTPSQQAHVTNVKDNPVQIAADAAEGAWRGFDEQETTVAVARYAPFNAIALLVGSQVGRPGVLTQCSLEEATELKLGMLGHTCYAETISVYGTEPVFTDGDDTPWSKGFLASSYASRGLKMRFTSGSGSEVQMGYAEGKSMLYLEARCIYITKAAGVQGLQNGSVSCIGVPSAVPSGIRAVLAENLICSSLDLECASSNDQTFTHSDMRRTARLLMQFLPGTDFISSGYSAVPNYDNMFAGSNEDAEDFDDYNVIQRDLKVDGGLRPVREEDVIAIRNKAARALQAVFAGMGLPPITDEEVEAATYAHGSKDMPERNIVEDIKFAQEIINKNRNGLEVVKALAQGGFTDVAQDMLNIQKAKLTGDYLHTSAIIVGDGQVLSAVNDVNDYAGPATGYRLQGERWEEIKNIPGALDPNEID

Source

organism	Klebsiella oxytoca
ncbi_taxonomy_id	571
host_organism	Escherichia coli

Entity 2 polymer

description	PROTEIN (DIOL DEHYDRATASE)
formula_weight	24141.7 kDa
ec_number	4.2.1.28
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

MEINEKLLRQIIEDVLSEMKGSDKPVSFNAPAASAAPQATPPAGDGFLTEVGEARQGTQQDEVIIAVGPAFGLAQTVNIVGIPHKSILREVIAGIEEEGIKARVIRCFKSSDVAFVAVEGNRLSGSGISIGIQSKGTTVIHQQGLPPLSNLELFPQAPLLTLETYRQIGKNAARYAKRESPQPVPTLNDQMARPKYQAKSAILHIKETKYVVTGKNPQELRVAL

Source

organism	Klebsiella oxytoca
ncbi_taxonomy_id	571
host_organism	Escherichia coli

Entity 3 polymer

description	PROTEIN (DIOL DEHYDRATASE)
formula_weight	19198.7 kDa
ec_number	4.2.1.28
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,M

MNTDAIESMVRDVLSRMNSLQGEAPAAAPAAGGASRSARVSDYPLANKHPEWVKTATNKTLDDFTLENVLSNKVTAQDMRITPETLRLQASIAKDAGRDRLAMNFERAAELTAVPDDRILEIYNALRPYRSTKEELLAIADDLESRYQAKICAAFVREAATLYVERKKLKGDD

Source

organism	Klebsiella oxytoca
ncbi_taxonomy_id	571
host_organism	Escherichia coli

Entity 4 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	S-1,2-PROPANEDIOL
formula_weight	76.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	COBALAMIN
formula_weight	1330.4 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	396

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6. Citations (1)

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length_a	76.200 Å
length_b	122.300 Å
length_c	209.600 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.200 Å
resolution_low	10.000 Å
r_factor	0.1880
r_work	0.1870
r_free	0.2360

fit	/app/data/saxs_computation/di/1dio/1dio.fit
pddf	/app/data/pr_computation/di/1dio/1dio.pr.out
profile	/app/data/saxs_computation/di/1dio/1dio.dat

DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

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

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)