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9qv1

1-Phosphofructokinase mutant K95H from E. coli with bound fructose 1-phosphate and ADP

Method: X-RAY DIFFRACTION D_max: 61.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qv1
deposition_date	2025-04-11
last_revision	2026-04-22
title	1-Phosphofructokinase mutant K95H from E. coli with bound fructose 1-phosphate and ADP
keywords	fructose, fructose-1-phosphate, fructose-6-phosphate, kinase, FruK, ATP, ADP, 1-phosphofructokinase, 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	19.75 Å
rg_electron	18.65 Å
i0	20587600.00
molecular_weight	34242.0 kDa
excluded_volume	42712 Å³
envelope_volume	48788 Å³
shell_volume	21249 Å³
envelope_diameter	61.2 Å
shell_rg	25.61 Å
envelope_rg	19.04 Å
shape_rg	18.66 Å
total_rg	19.53 Å
total_atoms	2403
n_residues	309
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	61.2 Å
rg_real	19.60 Å
rg_real_error	0.26 Å
i0_real	2.0590e+07
i0_real_error	2.4100e+05
rg_reciprocal	19.62 Å
i0_reciprocal	20590000.0000
total_estimate	0.8968
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.9 Å
skewness	0.136
kurtosis	-0.436
angular_range	— – 0.4050 Å⁻¹
current_alpha	0.0000
highest_alpha	5423000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.973

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	1-phosphofructokinase
formula_weight	33798.6 kDa
ec_number	2.7.1.56
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2674

MSRRVATITLNPAYDLVGFCPEIERGEVNLVKTTGLHAAGKGINVAKVLKDLGIDVTVGGFLGKDNQDGFQQLFSELGIANRFQVVQGRTRINVHLTEKDGEVTDFNFSGFEVTPADWERFVTDSLSWLGQFDMVCVSGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAAPWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLGAEGALWVNASGEWIAKPPSVDVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDRPQLAAMMARVDLQPFN

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	LITHIUM ION
formula_weight	6.9 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	1-O-phosphono-beta-D-fructofuranose
formula_weight	260.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	228

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6. Citations (1)

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length_a	62.980 Å
length_b	98.120 Å
length_c	139.850 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 2 2 2
int_tables_number	23
crystal_system	—

resolution	1.540 Å
resolution_low	19.700 Å
r_factor	0.1623
r_work	0.1618
r_free	0.1800

fit	/app/data/saxs_computation/qv/9qv1/9qv1.fit
pddf	/app/data/pr_computation/qv/9qv1/9qv1.pr.out
profile	/app/data/saxs_computation/qv/9qv1/9qv1.dat