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1f3f

STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX

Method: X-RAY DIFFRACTION D_max: 76.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1f3f
deposition_date	2000-06-02
title	STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX
keywords	NUCLEOSIDE DIPHOSPHATE KINASE, ANTI-HIV NUCLEOSIDE ANALOGUE, PHOSPHORYLATION, CH...O BOND, 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	24.93 Å
rg_electron	24.28 Å
i0	40773600.00
molecular_weight	49923.0 kDa
excluded_volume	62739 Å³
envelope_volume	72282 Å³
shell_volume	24833 Å³
envelope_diameter	77.7 Å
shell_rg	31.29 Å
envelope_rg	24.45 Å
shape_rg	24.30 Å
total_rg	25.02 Å
total_atoms	3510
n_residues	450
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	76.1 Å
rg_real	24.87 Å
rg_real_error	0.45 Å
i0_real	4.0770e+07
i0_real_error	5.4420e+05
rg_reciprocal	24.89 Å
i0_reciprocal	40770000.0000
total_estimate	0.9137
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	24.2 Å
skewness	0.186
kurtosis	-0.686
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	17440000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
formula_weight	16735.2 kDa
ec_number	2.7.4.6
mutation	H122G
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	3883

MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE

Source

organism	Dictyostelium discoideum
ncbi_taxonomy_id	44689
host_organism	Escherichia coli

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	;2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-TRIPHOSPHATE ;
formula_weight	464.2 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	;2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-DIPHOSPHATE ;
formula_weight	384.2 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	344

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6. Citations (1)

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length_a	70.018 Å
length_b	70.018 Å
length_c	152.098 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	18

space_group	P 31 2 1
int_tables_number	152
crystal_system	—

resolution	1.850 Å
resolution_low	29.730 Å
r_factor	0.2030
r_work	0.2030
r_free	0.2340

fit	/app/data/saxs_computation/f3/1f3f/1f3f.fit
pddf	/app/data/pr_computation/f3/1f3f/1f3f.pr.out
profile	/app/data/saxs_computation/f3/1f3f/1f3f.dat