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9sxb

Thermococcus sibiricus cyclic 2,3-diphosphoglycerate syntethase

Method: X-RAY DIFFRACTION D_max: 104.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sxb
deposition_date	2025-10-09
last_revision	2026-05-27
title	Thermococcus sibiricus cyclic 2,3-diphosphoglycerate syntethase
keywords	Syntethase, P-loop kinase fold, ATP binding protein, thermophiles, LYASE; LYASE
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	32.17 Å
rg_electron	31.60 Å
i0	135216000.00
molecular_weight	97051.0 kDa
excluded_volume	123660 Å³
envelope_volume	154690 Å³
shell_volume	40826 Å³
envelope_diameter	106.3 Å
shell_rg	38.44 Å
envelope_rg	31.69 Å
shape_rg	31.61 Å
total_rg	32.18 Å
total_atoms	6827
n_residues	868
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	104.5 Å
rg_real	32.23 Å
rg_real_error	0.65 Å
i0_real	1.3520e+08
i0_real_error	1.9790e+06
rg_reciprocal	32.21 Å
i0_reciprocal	135200000.0000
total_estimate	0.8846
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	36.3 Å
skewness	0.380
kurtosis	-0.453
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	44650000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.857

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Cyclic 2,3-diphosphoglycerate synthetase
formula_weight	48326.0 kDa
ec_number	6.5.1.9
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6895

TRMRMVLIDGEHYPDVTAWAIKKIGDVSCAVFLGGTEKIGDMKSLEEKIGVKLYYGESYISNIKKAINENKIGEVIDLSDEPVLNYEDRFRIAAVLLKHGIKYKGADFEFSPKEMVQINKPSLTILGTGKRVGKTAISGFVARTLKEISKPIIVTMGRGGPEEPEIIEGNKLEITPDFLVRVAESGKHAASDHFEDALTSRVITIGCRRCGGGMVGFSFFDIVNKGIKLAEKLEGDIVILEGSGATFPAVKADKYITVVGATQRIEFIKSYFGPFRIGLADLIVITLADMVSKEKIEKIQKIIESINPDAEIHLTAFKPRPLSEIKGKKAILVMTAPPEGLEKAARHLENRYDVEIVGKSANLANRPKLIEDLSRFKYYDTVLVELKAAAVDVATKEALKYGKEVIYIDNEPVNIDNKNLREAVLEIGWELKGERK

Source

organism	Thermococcus sibiricus
ncbi_taxonomy_id	172049
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	12

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	68

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6. Citations (1)

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length_a	162.460 Å
length_b	80.560 Å
length_c	82.740 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	2.280 Å
resolution_low	73.800 Å
r_factor	—
r_work	0.2186
r_free	0.2782

fit	/app/data/saxs_computation/sx/9sxb/9sxb.fit
pddf	/app/data/pr_computation/sx/9sxb/9sxb.pr.out
profile	/app/data/saxs_computation/sx/9sxb/9sxb.dat