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1e2d

Human thymidylate kinase complexed with thymidine monophosphate, adenosine diphosphate and a magnesium-ion

Method: X-RAY DIFFRACTION D_max: 53.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e2d
deposition_date	2000-05-22
title	Human thymidylate kinase complexed with thymidine monophosphate, adenosine diphosphate and a magnesium-ion
keywords	PHOSPHOTRANSFERASE, THYMIDYLATE KINASE, P-LOOP; PHOSPHOTRANSFERASE
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	17.64 Å
rg_electron	16.40 Å
i0	10980800.00
molecular_weight	24167.0 kDa
excluded_volume	30057 Å³
envelope_volume	33324 Å³
shell_volume	16800 Å³
envelope_diameter	52.9 Å
shell_rg	22.66 Å
envelope_rg	16.63 Å
shape_rg	16.40 Å
total_rg	17.39 Å
total_atoms	1697
n_residues	209
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	53.3 Å
rg_real	17.50 Å
rg_real_error	0.20 Å
i0_real	1.0980e+07
i0_real_error	1.3130e+05
rg_reciprocal	17.52 Å
i0_reciprocal	10980000.0000
total_estimate	0.7423
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	52.6 Å
skewness	0.092
kurtosis	-0.482
angular_range	— – 0.4500 Å⁻¹
current_alpha	0.0000
highest_alpha	2046000.0000
n_real_points	76
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 0.291; Positv: 1.000; Valcen: 0.985; Smooth: 0.988

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	THYMIDYLATE KINASE
formula_weight	24052.5 kDa
ec_number	2.7.4.9
mutation	YES
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1989

GSHMAARRGALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLRFPERSTEIGKLLSSYLQKKSDVEDHSVHLLFSANRWEQVPLIKEKLSQGVTLVVDRYAFSGVAFTGAKENFSLDWCKQPDVGLPKPDLVLFLQLQLADAAKRGAFGHERYENGAFQERALRCFHQLMKDTTLNWKMVDASKSIEAVHEDIRVLSEDAIATATEKPLGELWK

Source

organism	HOMO SAPIENS
common_name	HUMAN
ncbi_taxonomy_id	9606
host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

description	THYMIDINE-5'-PHOSPHATE
formula_weight	322.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

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

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	291

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6. Citations (1)

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length_a	101.000 Å
length_b	101.000 Å
length_c	49.800 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	1.650 Å
resolution_low	33.400 Å
r_factor	—
r_work	0.2010
r_free	0.2420

fit	/app/data/saxs_computation/e2/1e2d/1e2d.fit
pddf	/app/data/pr_computation/e2/1e2d/1e2d.pr.out
profile	/app/data/saxs_computation/e2/1e2d/1e2d.dat