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13ld

Deuterated alanine racemase from Geobacillus stearothermophilus

Method: X-RAY DIFFRACTION D_max: 126.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13ld
deposition_date	2026-05-12
last_revision	2026-06-10
title	Deuterated alanine racemase from Geobacillus stearothermophilus
keywords	deuterated, alanine racemase, isomerase, racemase; 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	39.22 Å
rg_electron	38.75 Å
i0	438097000.00
molecular_weight	172760.0 kDa
excluded_volume	217090 Å³
envelope_volume	275030 Å³
shell_volume	59303 Å³
envelope_diameter	131.3 Å
shell_rg	44.48 Å
envelope_rg	38.59 Å
shape_rg	38.76 Å
total_rg	39.05 Å
total_atoms	12189
n_residues	1517
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	126.5 Å
rg_real	39.13 Å
rg_real_error	0.76 Å
i0_real	4.3810e+08
i0_real_error	6.2090e+06
rg_reciprocal	39.19 Å
i0_reciprocal	438100000.0000
total_estimate	0.9010
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	47.5 Å
skewness	0.225
kurtosis	-0.552
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0001
highest_alpha	76360000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.913

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Alanine racemase
formula_weight	43823.0 kDa
ec_number	5.1.1.1
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	12757

MNDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGVYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAIGAGESSA

Source

organism	Geobacillus stearothermophilus 10
ncbi_taxonomy_id	272567
host_organism	Escherichia coli

Entity 2 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	483

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6. Citations (1)

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length_a	85.444 Å
length_b	109.925 Å
length_c	90.183 Å
angle_alpha	90.00 °
angle_beta	90.03 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.900 Å
resolution_low	27.810 Å
r_factor	0.1665
r_work	0.1644
r_free	0.2037

fit	/app/data/saxs_computation/3l/13ld/13ld.fit
pddf	/app/data/pr_computation/3l/13ld/13ld.pr.out
profile	/app/data/saxs_computation/3l/13ld/13ld.dat

Deuterated alanine racemase from Geobacillus stearothermophilus

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