← Back to search

9rcp

1,2-propanediol dehydratase with 0.1 % 1,3-propanediol additive

Method: X-RAY DIFFRACTION D_max: 147.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9rcp
deposition_date	2025-05-29
title	1,2-propanediol dehydratase with 0.1 % 1,3-propanediol additive
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	47.32 Å
rg_electron	46.60 Å
i0	1857940000.00
molecular_weight	355270.0 kDa
excluded_volume	442050 Å³
envelope_volume	559810 Å³
shell_volume	93996 Å³
envelope_diameter	148.8 Å
shell_rg	56.39 Å
envelope_rg	45.70 Å
shape_rg	46.59 Å
total_rg	46.95 Å
total_atoms	25024
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

▼

3. P(r) Analysis (GNOM)

dmax	147.9 Å
rg_real	46.98 Å
rg_real_error	0.83 Å
i0_real	1.8580e+09
i0_real_error	3.0440e+07
rg_reciprocal	47.31 Å
i0_reciprocal	1859000000.0000
total_estimate	0.8990
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	67.2 Å
skewness	0.034
kurtosis	-0.643
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0002
highest_alpha	380900000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.940

▶

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	26685

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	5

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1468

▶

6. Citations (1)

▶

length_a	81.435 Å
length_b	200.574 Å
length_c	118.108 Å
angle_alpha	90.00 °
angle_beta	106.59 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.900 Å
resolution_low	75.060 Å
r_factor	0.1878
r_work	0.1859
r_free	0.2233

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

1,2-propanediol dehydratase with 0.1 % 1,3-propanediol 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