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9wrf

Amino acid racemase in complex with PLP-L-Ile

Method: X-RAY DIFFRACTION D_max: 91.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wrf
deposition_date	2025-09-12
last_revision	2026-03-25
title	Amino acid racemase in complex with PLP-L-Ile
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	28.65 Å
rg_electron	27.58 Å
i0	156694000.00
molecular_weight	103760.0 kDa
excluded_volume	131580 Å³
envelope_volume	144020 Å³
shell_volume	41741 Å³
envelope_diameter	94.4 Å
shell_rg	36.60 Å
envelope_rg	27.94 Å
shape_rg	27.58 Å
total_rg	28.39 Å
total_atoms	7328
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	91.3 Å
rg_real	28.58 Å
rg_real_error	0.57 Å
i0_real	1.5670e+08
i0_real_error	2.1560e+06
rg_reciprocal	28.61 Å
i0_reciprocal	156700000.0000
total_estimate	0.8921
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.9 Å
skewness	0.309
kurtosis	-0.305
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	76690000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.945

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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	7364

MGSSHHHHHHSSGLVPRGSHMTKWDEIRKYTSKKIEKNLEIVKLDEKYIPRASGFKYYPMVIERSSGSRIWDKDGNEYIDFLTSAAVFNVGHTHPGVVKAVEEQIKKFFNYTMGYLYVEPPVRLAELLVEITPGNFEKKVTYGFSGSDAVDSSIKAARAYTKRVNIISFLHSYHGMTYGALSATGILDPKLKKLLHPMGNFHHVEFPDPYRNSWGIDGYEDPSELANRALDEIERKIKELNEDVAGIIIEPIQGDAGVVIPPEEFVRDLKKLTEEYGIVFIDEEVQTGMGRTGRWWGIEHFGVTPDLIVSAKALGGGMPISAVVGKAEIMDSVPVPFFVFTHIGHAVNASAAIATINVIKEEKLVERSEKLGEYMLKRLRELQETYPIIGDVRGKGLLIGVDIVKEGTREPDRSLAQKISWRAWEKGLIMITFGKHGNVLRIAPPLNIPQEDLDKGVEIIEESIKDAVEGKIPDEVLKFLRAW

Source

organism	Pyrococcus horikoshii
ncbi_taxonomy_id	53953
host_organism	Escherichia coli

Entity 2 non-polymer

description	(2S,3S)-3-methyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pentanoic acid
formula_weight	362.3 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	36

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6. Citations (1)

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length_a	63.644 Å
length_b	132.375 Å
length_c	136.525 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	2.870 Å
resolution_low	47.560 Å
r_factor	0.1896
r_work	0.1864
r_free	0.2581

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

Amino acid racemase in complex with PLP-L-Ile

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