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9quu

Triosephosphate isomerase of Rhodococcus sp. JG-3

Method: X-RAY DIFFRACTION D_max: 79.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9quu
deposition_date	2025-04-11
last_revision	2025-05-14
title	Triosephosphate isomerase of Rhodococcus sp. JG-3
keywords	psychrophile, eurypsychrophile, triosephosphate, isomerase, cold-active; 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	25.22 Å
rg_electron	24.37 Å
i0	47187900.00
molecular_weight	53671.0 kDa
excluded_volume	67505 Å³
envelope_volume	77514 Å³
shell_volume	26864 Å³
envelope_diameter	79.6 Å
shell_rg	31.52 Å
envelope_rg	24.56 Å
shape_rg	24.38 Å
total_rg	25.16 Å
total_atoms	3787
n_residues	514
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	79.0 Å
rg_real	25.24 Å
rg_real_error	0.54 Å
i0_real	4.7190e+07
i0_real_error	6.1180e+05
rg_reciprocal	25.23 Å
i0_reciprocal	47190000.0000
total_estimate	0.8111
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	30.1 Å
skewness	0.379
kurtosis	-0.477
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	14550000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.659; Stabil: 0.884; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.931

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Triosephosphate isomerase
formula_weight	27224.0 kDa
ec_number	5.3.1.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4115

MARKPLIAGNWKMNLNHLEAISLVQKIAFSLPEKYFDKVDVTVIPPFTDIRSVQTLIEGDKLLLTYGAQDVSAEDSGAFTGEISGSMLAKLGCTFVVVGHSERRTLHSEDDAVVLAKTKAALKNGLTPIVCIGEGLNIREAGEHVAYNVAQLRGSLDGLSADDIAKVVIAYEPVWAIGTGRVASASDAQEVCGAIREELKELASAEVAAGVRVLYGGSVNAKNVGEIVGQPDVDGALVGGASLKADEFATLSAIAAGGPLP

Source

organism	Rhodococcus sp. JG-3
ncbi_taxonomy_id	1305835
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	328

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6. Citations (1)

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length_a	86.102 Å
length_b	86.102 Å
length_c	152.835 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 43 21 2
int_tables_number	96
crystal_system	tetragonal

resolution	1.630 Å
resolution_low	47.620 Å
r_factor	0.1947
r_work	0.1942
r_free	0.2127

fit	/app/data/saxs_computation/qu/9quu/9quu.fit
pddf	/app/data/pr_computation/qu/9quu/9quu.pr.out
profile	/app/data/saxs_computation/qu/9quu/9quu.dat

Triosephosphate isomerase of Rhodococcus sp. JG-3

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