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9wr1

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

Method: X-RAY DIFFRACTION D_max: 118.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wr1
deposition_date	2025-09-11
last_revision	2026-03-25
title	Ala/Ser-specific racemase in complex with PLP-L-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	37.22 Å
rg_electron	36.56 Å
i0	547608000.00
molecular_weight	203690.0 kDa
excluded_volume	260020 Å³
envelope_volume	297150 Å³
shell_volume	64239 Å³
envelope_diameter	131.9 Å
shell_rg	45.28 Å
envelope_rg	36.93 Å
shape_rg	36.53 Å
total_rg	37.14 Å
total_atoms	14370
n_residues	1832
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	118.3 Å
rg_real	37.11 Å
rg_real_error	0.75 Å
i0_real	5.4760e+08
i0_real_error	8.4620e+06
rg_reciprocal	37.18 Å
i0_reciprocal	547600000.0000
total_estimate	0.9007
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	42.2 Å
skewness	0.233
kurtosis	-0.579
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	582400000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.947

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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	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	14642

MGSSHHHHHHSSGLVPRGSHMEYPKIVVKPPGPRAKELIEREKKVLSTGIGVKLFPLVPKRGFGPFIEDVDGNVFIDFLAGAAAASTGYAHPKLVKAVKEQVELIQHSMIGYTHSERAIRVAEKLVEISPIENSKVIFGLSGSDAVDMAIKVSKFSTRRPWILAFIGAYHGQTLGATSVASFQVSQKRGYSPLMPNVFWIPYPNPFRNIWGINGYEEPDELINRVLDYLEYYVFSHVVPPDEVAALFAEPIQGDAGIVVPPENFFKELKKLLEEYGILLVMDEVQTGIGRTGKWFASEWFNVKPDMIIFGKGVASGMGLSGVIGRKEIMDITSGSALLTPAANPVISAAAEATLEIIEEENLLKNALEVGEFIMGRLKEIKERFEIIGDVRGKGLMIGVEIVKENGRPDPEMTGKICWRAFELGLILPSYGMFGNVIRITPPLVLTKEVAEKALEIIERAIKDTLTGKVERKVVTWH

Source

organism	Pyrococcus horikoshii
ncbi_taxonomy_id	53953
host_organism	Escherichia coli

Entity 2 non-polymer

description	ALANYL-PYRIDOXAL-5'-PHOSPHATE
formula_weight	320.2 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	272

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6. Citations (1)

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length_a	58.184 Å
length_b	150.203 Å
length_c	104.085 Å
angle_alpha	90.00 °
angle_beta	100.70 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.400 Å
resolution_low	48.460 Å
r_factor	0.2122
r_work	0.2096
r_free	0.2596

fit	/app/data/saxs_computation/wr/9wr1/9wr1.fit
pddf	/app/data/pr_computation/wr/9wr1/9wr1.pr.out
profile	/app/data/saxs_computation/wr/9wr1/9wr1.dat

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