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9wu1

Amino acid racemase in complex with PLP-D-Phe

Method: X-RAY DIFFRACTION D_max: 91.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wu1
deposition_date	2025-09-17
title	Amino acid racemase in complex with PLP-D-Phe
keywords	racemase, fold type 1, 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	28.42 Å
rg_electron	27.61 Å
i0	314086000.00
molecular_weight	96382.0 kDa
excluded_volume	94000 Å³
envelope_volume	144700 Å³
shell_volume	41858 Å³
envelope_diameter	94.8 Å
shell_rg	36.61 Å
envelope_rg	28.01 Å
shape_rg	27.59 Å
total_rg	28.21 Å
total_atoms	7334
n_residues	918
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	91.6 Å
rg_real	28.33 Å
rg_real_error	0.54 Å
i0_real	3.1410e+08
i0_real_error	4.6070e+06
rg_reciprocal	28.36 Å
i0_reciprocal	314100000.0000
total_estimate	0.8705
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.3 Å
skewness	0.315
kurtosis	-0.289
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	97110000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.721

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Broad substrate specificity amino-acid racemase
formula_weight	54317.1 kDa
ec_number	5.1.1.10
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7590

MGSSHHHHHHSSGLVPRGSHMTKWDEIRKYTSKKIEKNLEIVKLDEKYIPRASGFKYYPMVIERSSGSRIWDKDGNEYIDFLTSAAVFNVGHTHPGVVKAVEEQIKKFFNYTMGYLYVEPPVRLAELLVEITPGNFEKKVTYGFSGSDAVDSSIKAARAYTKRVNIISFLHSYHGMTYGALSATGILDPKLKKLLHPMGNFHHVEFPDPYRNSWGIDGYEDPSELANRALDEIERKIKELNEDVAGIIIEPIQGDAGVVIPPEEFVRDLKKLTEEYGIVFIDEEVQTGMGRTGRWWGIEHFGVTPDLIVSAKALGGGMPISAVVGKAEIMDSVPVPFFVFTHIGHAVNASAAIATINVIKEEKLVERSEKLGEYMLKRLRELQETYPIIGDVRGKGLLIGVDIVKEGTREPDRSLAQKISWRAWEKGLIMITFGKHGNVLRIAPPLNIPQEDLDKGVEIIEESIKDAVEGKIPDEVLKFLRAW

Source

organism	Pyrococcus horikoshii
ncbi_taxonomy_id	53953
host_organism	Escherichia coli

Entity 2 non-polymer

description	(2~{R})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-phenyl-propanoic acid
formula_weight	396.3 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	250

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6. Citations (1)

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length_a	63.901 Å
length_b	133.203 Å
length_c	135.360 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.100 Å
resolution_low	46.510 Å
r_factor	0.1698
r_work	0.1681
r_free	0.1998

fit	/app/data/saxs_computation/wu/9wu1/9wu1.fit
pddf	/app/data/pr_computation/wu/9wu1/9wu1.pr.out
profile	/app/data/saxs_computation/wu/9wu1/9wu1.dat

Amino acid racemase in complex with PLP-D-Phe

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