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9rco

1,2-propanediol dehydratase with 0.1 % glycerol additive

Method: X-RAY DIFFRACTION D_max: 146.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rco
deposition_date	2025-05-29
title	1,2-propanediol dehydratase with 0.1 % glycerol additive
keywords	glycyl radical enzyme, 1, 2-propanediol, 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	47.21 Å
rg_electron	46.50 Å
i0	1859740000.00
molecular_weight	355320.0 kDa
excluded_volume	442100 Å³
envelope_volume	557390 Å³
shell_volume	93935 Å³
envelope_diameter	148.6 Å
shell_rg	56.09 Å
envelope_rg	45.59 Å
shape_rg	46.48 Å
total_rg	46.83 Å
total_atoms	25028
n_residues	3172
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	146.6 Å
rg_real	46.88 Å
rg_real_error	0.77 Å
i0_real	1.8600e+09
i0_real_error	3.1040e+07
rg_reciprocal	47.21 Å
i0_reciprocal	1860000000.0000
total_estimate	0.8988
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	66.6 Å
skewness	0.037
kurtosis	-0.642
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0001
highest_alpha	370100000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.911

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Glycyl radical protein
formula_weight	91569.9 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	27369

MGSSHHHHHHSQDHENLYFQGSMGLEKGFTHPTDRVVRLKNMILHAKPYVESERAVLATEAYKENEQLPAIMRRAKVVEKIFNELPVTIRPDELIVGAVTINPRSTEICPEFSYDWVEKEFDTMAHRVADPFIIEKKTADELHQAFKYWPGKTTSSLAASYMSEGTKESMSNGVFTVGNYFFGGIGHVSVDYGKVLKIGFRGIIDEVTRALENLDRSTSDYIKKEQFYNAVILSYQAAINFAHRYAQEASRLAREERDPTRQRELEQIASNCTRVPEYGATTFWEACQTFWFIQSMLQIESSGHSISPGRFDQYMYPYLAADTAISSEFAQELVDCCWIKLNDINKTRDEISAQAFAGYAVFQNLCVGGQTEDGRDATNPLTYMCMEATAHVRLPQPSFSIRVWQGTPDEFLYRACELVRLGLGVPAMYNDEVIIPALQNRGVSLHDARDYCIIGCVEPQAPHRTEGWHDAAFFNVAKVLEITLNNGRSGNKQLGPMTGEMTQYAGMDDFYAAFKKQMAHFVHQLVEACNSVDIAHGERCPLPFLSALVDDCIGRGKSLQEGGAIYNFTGPQAFGIADTGDSVYAIQKQVFEDRRLTLQELKGALDANFGYRSGNPRYEEIRHILENSPCFGNDIDDVDLVARQCALIYCQEVEKYTNPRGGRFQAGIYPVSANVLFGKDVSALPDGRLAKEPLADGVSPRQGKDTLGPTAAANSVAKLDHFIASNGTLYNQKFLPSSLAGEKGLRNFGGLVRNYFDKKGMHVQFNVIDRNTLLEAQKNPQQHQDLVVRVAGYSAQFVVLAKEVQDDIISRTEQQF

Source

organism	Raoultella planticola
ncbi_taxonomy_id	575
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2155

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6. Citations (1)

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length_a	81.529 Å
length_b	199.413 Å
length_c	118.100 Å
angle_alpha	90.00 °
angle_beta	107.02 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.700 Å
resolution_low	72.610 Å
r_factor	0.1831
r_work	0.1816
r_free	0.2112

fit	/app/data/saxs_computation/rc/9rco/9rco.fit
pddf	/app/data/pr_computation/rc/9rco/9rco.pr.out
profile	/app/data/saxs_computation/rc/9rco/9rco.dat

1,2-propanediol dehydratase with 0.1 % glycerol additive

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