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1e9c

Mutant human thymidylate kinase complexed with TMP and APPNP

Method: X-RAY DIFFRACTION D_max: 53.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e9c
deposition_date	2000-10-10
title	Mutant human thymidylate kinase complexed with TMP and APPNP
keywords	PHOSPHOTRANSFERASE, THYMIDYLATE KINASE, P-LOOP, 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	17.46 Å
rg_electron	16.34 Å
i0	11962000.00
molecular_weight	24854.0 kDa
excluded_volume	30716 Å³
envelope_volume	33387 Å³
shell_volume	16833 Å³
envelope_diameter	53.4 Å
shell_rg	22.73 Å
envelope_rg	16.61 Å
shape_rg	16.34 Å
total_rg	17.29 Å
total_atoms	1741
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	53.5 Å
rg_real	17.33 Å
rg_real_error	0.30 Å
i0_real	1.1960e+07
i0_real_error	1.3390e+05
rg_reciprocal	17.35 Å
i0_reciprocal	11960000.0000
total_estimate	0.8245
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.1 Å
skewness	0.098
kurtosis	-0.449
angular_range	— – 0.4550 Å⁻¹
current_alpha	0.0000
highest_alpha	1485000.0000
n_real_points	76
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	THYMIDYLATE KINASE
formula_weight	24140.7 kDa
ec_number	2.7.4.9
mutation	YES
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2018

GSHMAARRGALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLRFPERSTEIGKLLSSYLQKKSDVEDHSVHLLFSANRWEQVPLIKEKLSQGVTLVVDRYAFSGVAYTGAKENFSLDWCKQPDVGLPKPDLVLFLQLQLADAAKRGAFGHERYENGAFQERALRCFHQLMKDTTLNWKMVDASKSIEAVHEDIRVLSEDAIATATEKPLKELWK

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	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	262

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6. Citations (2)

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length_a	101.300 Å
length_b	101.300 Å
length_c	49.200 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	1.600 Å
resolution_low	70.000 Å
r_factor	—
r_work	0.2090
r_free	0.2680

fit	/app/data/saxs_computation/e9/1e9c/1e9c.fit
pddf	/app/data/pr_computation/e9/1e9c/1e9c.pr.out
profile	/app/data/saxs_computation/e9/1e9c/1e9c.dat