Central domain of Glucan Water Dikinase-1 in alternative closed conformation

Method: X-RAY DIFFRACTION D_max: 72.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qvi
deposition_date	2025-04-11
title	Central domain of Glucan Water Dikinase-1 in alternative closed conformation
keywords	starch, dikinase, phosphorylation, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
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	23.71 Å
rg_electron	22.59 Å
i0	41544000.00
molecular_weight	49178.0 kDa
excluded_volume	61336 Å³
envelope_volume	73616 Å³
shell_volume	26969 Å³
envelope_diameter	75.4 Å
shell_rg	29.76 Å
envelope_rg	22.63 Å
shape_rg	22.60 Å
total_rg	23.41 Å
total_atoms	3462
n_residues	444
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	72.8 Å
rg_real	23.56 Å
rg_real_error	0.33 Å
i0_real	4.1540e+07
i0_real_error	4.9600e+05
rg_reciprocal	23.60 Å
i0_reciprocal	41540000.0000
total_estimate	0.7116
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	29.6 Å
skewness	0.133
kurtosis	-0.515
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	12030000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 0.154; Positv: 1.000; Valcen: 0.993; Smooth: 0.977

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

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6. Citations (1)

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length_a	94.134 Å
length_b	94.134 Å
length_c	150.757 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	3.250 Å
resolution_low	47.111 Å
r_factor	—
r_work	0.2607
r_free	0.3061

description	Alpha-glucan water dikinase, chloroplastic
formula_weight	52457.5 kDa
ec_number	2.7.13.3,2.7.9.4
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	3462

Central domain of Glucan Water Dikinase-1 in alternative closed conformation

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

5. Entities & Polymer Info (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Solanum tuberosum
common_name	potato
ncbi_taxonomy_id	4113
host_organism	Escherichia coli

fit	/app/data/saxs_computation/qv/9qvi/9qvi.fit
pddf	/app/data/pr_computation/qv/9qvi/9qvi.pr.out
profile	/app/data/saxs_computation/qv/9qvi/9qvi.dat