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9wqz

Ala/Ser-specific racemase in complex with PLP-D-Ala

Method: X-RAY DIFFRACTION D_max: 69.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wqz
deposition_date	2025-09-11
last_revision	2026-03-25
title	Ala/Ser-specific racemase in complex with PLP-D-Ala
keywords	fold type 1, racemase, ISOMERASE; ISOMERASE
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	23.12 Å
rg_electron	21.99 Å
i0	38331900.00
molecular_weight	50840.0 kDa
excluded_volume	64922 Å³
envelope_volume	74181 Å³
shell_volume	27304 Å³
envelope_diameter	70.7 Å
shell_rg	29.44 Å
envelope_rg	22.19 Å
shape_rg	21.99 Å
total_rg	22.90 Å
total_atoms	3586
n_residues	457
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	69.4 Å
rg_real	22.98 Å
rg_real_error	0.33 Å
i0_real	3.8330e+07
i0_real_error	4.4840e+05
rg_reciprocal	23.02 Å
i0_reciprocal	38330000.0000
total_estimate	0.9087
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.8 Å
skewness	0.153
kurtosis	-0.486
angular_range	— – 0.3450 Å⁻¹
current_alpha	0.0000
highest_alpha	7165000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.973

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Alanine/serine racemase
formula_weight	52755.0 kDa
ec_number	5.1.1.-,5.1.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3650

MGSSHHHHHHSSGLVPRGSHMEYPKIVVKPPGPRAKELIEREKKVLSTGIGVKLFPLVPKRGFGPFIEDVDGNVFIDFLAGAAAASTGYAHPKLVKAVKEQVELIQHSMIGYTHSERAIRVAEKLVEISPIENSKVIFGLSGSDAVDMAIKVSKFSTRRPWILAFIGAYHGQTLGATSVASFQVSQKRGYSPLMPNVFWIPYPNPFRNIWGINGYEEPDELINRVLDYLEYYVFSHVVPPDEVAALFAEPIQGDAGIVVPPENFFKELKKLLEEYGILLVMDEVQTGIGRTGKWFASEWFNVKPDMIIFGKGVASGMGLSGVIGRKEIMDITSGSALLTPAANPVISAAAEATLEIIEEENLLKNALEVGEFIMGRLKEIKERFEIIGDVRGKGLMIGVEIVKENGRPDPEMTGKICWRAFELGLILPSYGMFGNVIRITPPLVLTKEVAEKALEIIERAIKDTLTGKVERKVVTWH

Source

organism	Pyrococcus horikoshii
ncbi_taxonomy_id	53953
host_organism	Escherichia coli

Entity 2 non-polymer

description	N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE
formula_weight	320.2 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	64

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6. Citations (1)

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length_a	100.793 Å
length_b	100.793 Å
length_c	159.261 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 4 2 2
int_tables_number	97
crystal_system	—

resolution	2.160 Å
resolution_low	47.010 Å
r_factor	0.1844
r_work	0.1817
r_free	0.2381

fit	/app/data/saxs_computation/wq/9wqz/9wqz.fit
pddf	/app/data/pr_computation/wq/9wqz/9wqz.pr.out
profile	/app/data/saxs_computation/wq/9wqz/9wqz.dat

Ala/Ser-specific racemase in complex with PLP-D-Ala

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