← Back to search

9rcq

1,2-propanediol dehydratase with no ligand additives

Method: X-RAY DIFFRACTION D_max: 147.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9rcq
deposition_date	2025-05-29
title	1,2-propanediol dehydratase with no ligand additives
keywords	glycyl radical enzyme, 1, 2-propanediol, LYASE; LYASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	47.42 Å
rg_electron	46.70 Å
i0	1883010000.00
molecular_weight	357300.0 kDa
excluded_volume	444390 Å³
envelope_volume	561660 Å³
shell_volume	94214 Å³
envelope_diameter	145.1 Å
shell_rg	56.37 Å
envelope_rg	45.76 Å
shape_rg	46.69 Å
total_rg	47.03 Å
total_atoms	25170
n_residues	3189
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

▼

3. P(r) Analysis (GNOM)

dmax	147.1 Å
rg_real	47.09 Å
rg_real_error	0.85 Å
i0_real	1.8830e+09
i0_real_error	3.2110e+07
rg_reciprocal	47.42 Å
i0_reciprocal	1884000000.0000
total_estimate	0.8993
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	66.8 Å
skewness	0.035
kurtosis	-0.647
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0001
highest_alpha	386900000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.914

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

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	25432

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 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	134

▶

6. Citations (1)

▶

length_a	131.890 Å
length_b	131.890 Å
length_c	457.930 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 31 2 1
int_tables_number	152
crystal_system	trigonal

resolution	2.600 Å
resolution_low	76.320 Å
r_factor	0.1912
r_work	0.1888
r_free	0.2379

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

1,2-propanediol dehydratase with no ligand additives

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