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1eex

CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

Method: X-RAY DIFFRACTION D_max: 123.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1eex
deposition_date	2000-02-04
title	CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN 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	37.23 Å
rg_electron	36.93 Å
i0	565491000.00
molecular_weight	192910.0 kDa
excluded_volume	240680 Å³
envelope_volume	276160 Å³
shell_volume	60280 Å³
envelope_diameter	124.5 Å
shell_rg	44.80 Å
envelope_rg	37.33 Å
shape_rg	36.95 Å
total_rg	37.26 Å
total_atoms	13530
n_residues	1732
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	123.0 Å
rg_real	37.25 Å
rg_real_error	1.16 Å
i0_real	5.6550e+08
i0_real_error	1.0580e+07
rg_reciprocal	37.24 Å
i0_reciprocal	565500000.0000
total_estimate	0.8817
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.0 Å
skewness	0.372
kurtosis	-0.445
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	153500000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.922

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	PROPANEDIOL 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	15494

MRSKRFEALAKRPVNQDGFVKEWIEEGFIAMESPNDPKPSIKIVNGAVTELDGKPVSDFDLIDHFIARYGINLNRAEEVMAMDSVKLANMLCDPNVKRSEIVPLTTAMTPAKIVEVVSHMNVVEMMMAMQKMRARRTPSQQAHVTNVKDNPVQIAADAAEGAWRGFDEQETTVAVARYAPFNAIALLVGSQVGRPGVLTQCSLEEATELKLGMLGHTCYAETISVYGTEPVFTDGDDTPWSKGFLASSYASRGLKMRFTSGSGSEVQMGYAEGKSMLYLEARCIYITKAAGVQGLQNGSVSCIGVPSAVPSGIRAVLAENLICSSLDLECASSNDQTFTHSDMRRTARLLMQFLPGTDFISSGYSAVPNYDNMFAGSNEDAEDFDDYNVIQRDLKVDGGLRPVREEDVIAIRNKAARALQAVFAGMGLPPITDEEVEAATYAHGSKDMPERNIVEDIKFAQEIINKNRNGLEVVKALAQGGFTDVAQDMLNIQKAKLTGDYLHTSAIIVGDGQVLSAVNDVNDYAGPATGYRLQGERWEEIKNIPGALDPNEID

Source

organism	Klebsiella oxytoca
ncbi_taxonomy_id	571
host_organism	Escherichia coli

Entity 2 polymer

description	PROPANEDIOL 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	PROPANEDIOL 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	4

Entity 5 non-polymer

description	CO-(ADENIN-9-YL-PENTYL)-COBALAMIN
formula_weight	1537.6 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

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

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1872

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6. Citations (2)

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length_a	73.380 Å
length_b	121.400 Å
length_c	207.600 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	1.700 Å
resolution_low	30.000 Å
r_factor	0.1640
r_work	0.1610
r_free	0.2260

fit	/app/data/saxs_computation/ee/1eex/1eex.fit
pddf	/app/data/pr_computation/ee/1eex/1eex.pr.out
profile	/app/data/saxs_computation/ee/1eex/1eex.dat

CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN 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

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 (2)

7. Files & Curves (10)

Files (7)

Curves (3)