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9vqk

crystal structure of an (R)-selective omega-transaminase from Ancylobacter lacus

Method: X-RAY DIFFRACTION D_max: 102.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vqk
deposition_date	2025-07-05
last_revision	2026-02-04
title	crystal structure of an (R)-selective omega-transaminase from Ancylobacter lacus
keywords	(R)-selective omega-transaminase, Complex with PLP, 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	32.87 Å
rg_electron	32.19 Å
i0	315155000.00
molecular_weight	142640.0 kDa
excluded_volume	178250 Å³
envelope_volume	202670 Å³
shell_volume	50511 Å³
envelope_diameter	110.6 Å
shell_rg	40.50 Å
envelope_rg	32.38 Å
shape_rg	32.21 Å
total_rg	32.72 Å
total_atoms	10028
n_residues	1273
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	102.7 Å
rg_real	32.71 Å
rg_real_error	0.54 Å
i0_real	3.1520e+08
i0_real_error	4.7010e+06
rg_reciprocal	32.78 Å
i0_reciprocal	315200000.0000
total_estimate	0.9002
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	100.6 Å
skewness	0.202
kurtosis	-0.482
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	96440000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.913

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Omega-Transaminase
formula_weight	35675.8 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,D,F,H
atom_count	11002

MSSMEAVFAGYQTRLEALKASDNPFAAGIAWVAGELTPLADARMPLMDQGFLRSDLTYDVPAIWDGRFFRLHDHLDRMERSCEKLRLRCPLGREELCGTLVGMAAKSGIRDGFVFLAVTRGLKQVRGNRPEDLTNNLYMFISPYVWVVSPEMQRTGAPAIVTRTVRRTPPGAFDPTVKNLQWGDFTRGLMEAQDRGAIYPILTDGDGNLTEGAGYNVVLVKDGVLYTPERGVLEGITRKTVMEIAAARGIDVRMEHVPVDLAYRADELFFCTTAAGIMPVTTLDGVRVGGGQVGPITRQIWEDYWDLHYDPKLTIEVPYR

Source

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

Entity 2 non-polymer

description	PYRIDOXAL-5'-PHOSPHATE
formula_weight	247.1 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	974

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6. Citations (1)

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length_a	77.968 Å
length_b	82.619 Å
length_c	197.688 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.020 Å
resolution_low	19.970 Å
r_factor	0.2011
r_work	0.1986
r_free	0.2503

fit	/app/data/saxs_computation/vq/9vqk/9vqk.fit
pddf	/app/data/pr_computation/vq/9vqk/9vqk.pr.out
profile	/app/data/saxs_computation/vq/9vqk/9vqk.dat

crystal 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