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9wf1

PLP and 1-Boc-2-methyl-piperidin-5-one complex structure of an (R)-selective omega-transaminase from Ancylobacter lacus

Method: X-RAY DIFFRACTION D_max: 105.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wf1
deposition_date	2025-08-20
last_revision	2026-02-04
title	PLP and 1-Boc-2-methyl-piperidin-5-one complex structure of an (R)-selective omega-transaminase from Ancylobacter lacus
keywords	(R)-selective omega-transaminase, Complex with PLP and 1-Boc-2-methyl-piperidin-5-one, TRANSFERASE; TRANSFERASE
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	33.47 Å
rg_electron	33.00 Å
i0	612232000.00
molecular_weight	132940.0 kDa
excluded_volume	128090 Å³
envelope_volume	213410 Å³
shell_volume	52107 Å³
envelope_diameter	111.3 Å
shell_rg	41.13 Å
envelope_rg	33.00 Å
shape_rg	33.00 Å
total_rg	33.41 Å
total_atoms	10054
n_residues	1267
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	105.4 Å
rg_real	33.34 Å
rg_real_error	0.72 Å
i0_real	6.1220e+08
i0_real_error	8.8710e+06
rg_reciprocal	33.42 Å
i0_reciprocal	612300000.0000
total_estimate	0.9018
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	40.4 Å
skewness	0.192
kurtosis	-0.511
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	112600000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.939

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Omega-Transaminase
formula_weight	35903.9 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,D,F,H
atom_count	11244

MSSMEAVFAGYQTRLEALKASDNPFAAGIAWVAGELTPLADARMPLMDQGFLRSDLTYDVPAIWDGRFFRLHDHLDRMERSCEKLRLRCPLGREELCGTLVGMAAKSGIRDGFVFLAVTRGLKQVRGNRPEDLTNNLYMFISPYVWVVSPEMQRTGAPAIVTRTVRRTPPGAFDPTVKNLQWGDFTRGLMEAQDRGAIYPILTDGDGNLTEGAGYNVVLVKDGVLYTPERGVLEGITRKTVMEIAAARGIDVRMEHVPVDLAYRADELFFCTTAAGIMPVTTLDGVRVGGGQVGPITRQIWEDYWDLHYDPKLTIEVPYR

Source

organism	Ancylobacter lacus
ncbi_taxonomy_id	2579970
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	~{tert}-butyl (2~{S})-2-methyl-5-oxidanylidene-piperidine-1-carboxylate
formula_weight	213.3 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1190

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6. Citations (1)

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length_a	65.830 Å
length_b	72.450 Å
length_c	84.320 Å
angle_alpha	74.64 °
angle_beta	85.69 °
angle_gamma	69.92 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.930 Å
resolution_low	23.390 Å
r_factor	0.1883
r_work	0.1876
r_free	0.2242

fit	/app/data/saxs_computation/wf/9wf1/9wf1.fit
pddf	/app/data/pr_computation/wf/9wf1/9wf1.pr.out
profile	/app/data/saxs_computation/wf/9wf1/9wf1.dat

PLP and 1-Boc-2-methyl-piperidin-5-one complex structure of an (R)-selective omega-transaminase from Ancylobacter lacus

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