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9pyu

E. Coli Glucokinase - K216Q

Method: X-RAY DIFFRACTION D_max: 87.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pyu
deposition_date	2025-08-08
last_revision	2026-05-13
title	E. Coli Glucokinase - K216Q
keywords	chemical modification, binding properties, TRANSFERASE; TRANSFERASE
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	27.86 Å
rg_electron	26.91 Å
i0	75900300.00
molecular_weight	69326.0 kDa
excluded_volume	87281 Å³
envelope_volume	106980 Å³
shell_volume	33362 Å³
envelope_diameter	90.1 Å
shell_rg	34.25 Å
envelope_rg	26.95 Å
shape_rg	26.89 Å
total_rg	27.75 Å
total_atoms	4884
n_residues	640
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	87.1 Å
rg_real	27.77 Å
rg_real_error	0.42 Å
i0_real	7.5900e+07
i0_real_error	9.6180e+05
rg_reciprocal	27.80 Å
i0_reciprocal	75900000.0000
total_estimate	0.9024
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	35.1 Å
skewness	0.256
kurtosis	-0.426
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	18490000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.904

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Glucokinase
formula_weight	34633.8 kDa
ec_number	2.7.1.2
mutation	K216Q
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4973

TKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPQDITERALADSCTDCRRALSLFCVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNPGLLGSGAHLRQTLGHIL

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	89

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6. Citations (1)

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length_a	85.088 Å
length_b	85.088 Å
length_c	183.319 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	2.440 Å
resolution_low	28.720 Å
r_factor	0.1808
r_work	0.1785
r_free	0.2248

fit	/app/data/saxs_computation/py/9pyu/9pyu.fit
pddf	/app/data/pr_computation/py/9pyu/9pyu.pr.out
profile	/app/data/saxs_computation/py/9pyu/9pyu.dat

E. Coli Glucokinase - K216Q

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