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9vmk

Crystal structure of TeGH116 from Thermosynechococcus elongatus with glucose

Method: X-RAY DIFFRACTION D_max: 140.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vmk
deposition_date	2025-06-28
last_revision	2025-11-26
title	Crystal structure of TeGH116 from Thermosynechococcus elongatus with glucose
keywords	TeGH116, beta-glucosidase, Thermosynechococcus elongatus, cyanobacteria, HYDROLASE, glucose; HYDROLASE
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	43.17 Å
rg_electron	42.98 Å
i0	456978000.00
molecular_weight	177620.0 kDa
excluded_volume	221870 Å³
envelope_volume	268650 Å³
shell_volume	51552 Å³
envelope_diameter	146.2 Å
shell_rg	48.34 Å
envelope_rg	42.58 Å
shape_rg	42.99 Å
total_rg	43.17 Å
total_atoms	12575
n_residues	1570
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	140.3 Å
rg_real	43.33 Å
rg_real_error	1.02 Å
i0_real	4.5700e+08
i0_real_error	7.3180e+06
rg_reciprocal	43.17 Å
i0_reciprocal	456900000.0000
total_estimate	0.8459
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.1 Å
skewness	0.311
kurtosis	-0.780
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0001
highest_alpha	188300000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.889; Smooth: 0.654

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Tlr0193 protein
formula_weight	90460.2 kDa
ec_number	3.2.1.21
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	13216

AMAMPSDGAALKRYSGSGASSENGVIEFANCAWTRAIGQGWETPYRVRYASNLDDGPWYGMPLGGFGAGCIGRSSAGDFNLWHVDGGEHIFGTLPACQFSLFEQGEQTQAYALGSAPKDGRLSSWQWYPAGKGTYAVRYPRSWFVYEGVFRAQITCEQFSPILPHNYQETSYPVAVFLWTFSNPTDQSLTLSLMLSWQNTVGWFCNTTPSSAIAIRDDGSPVYTYTPRWGQSDGNFNELIQTESFQGWRLRRMPHPNPPQEGDGEWAALIPTGLGEFFGCSRWQPEGDGAHLWQSFSVDGSLPFVNDPTPAAAGEQVAAAFALRFSLAPGERKQIPVVLAWDFPVTEFGKGVIYYRRYTDFCDRHGTNAVTLAAQALAAYATWQEQIRTWQAPILSHPDWPDWFKMALCNELYVLSSGGSLWSAASDRDPVGQFAVLECLDYRWYESLDVRLYGSFALLQLWPELEKSVMRAFARAIPTADPTLRIIGYFYRGDPETAYKAPRKLANAVPHDLGAPNEHPWEKTNYTAYQDCNLWKDLASDFVLLVYRDFLFTGGTDLNFARECWPAVVAALDHLKQFDQDGDGLPENGGAPDQTYDDWKLQGVSAYCGGLWLAALEAAIALGTLLQQPQVEIYRQWLSQARPRYHQLLWNGEYYRLDTGSGSDVIMADQLCGQFYAQLLGLVDIVPPDCCDRALRKIYDTCFLKFHNGQFGAANGLLPNGQPENPHATHPLEVWTGINFGLAAFLWQRGMIDEAWRLAEVVVRQIYENGLQFRTPEAITANGTFRACMYLRPMAIWALALVSGGSRLP

Source

organism	Thermosynechococcus vestitus BP-1
ncbi_taxonomy_id	197221
host_organism	Escherichia coli

Entity 2 non-polymer

description	beta-D-glucopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	9

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	L(+)-TARTARIC ACID
formula_weight	150.1 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	617

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6. Citations (1)

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length_a	268.999 Å
length_b	55.094 Å
length_c	181.996 Å
angle_alpha	90.00 °
angle_beta	131.86 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.000 Å
resolution_low	26.535 Å
r_factor	—
r_work	0.1694
r_free	0.1894

fit	/app/data/saxs_computation/vm/9vmk/9vmk.fit
pddf	/app/data/pr_computation/vm/9vmk/9vmk.pr.out
profile	/app/data/saxs_computation/vm/9vmk/9vmk.dat