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1e2j

The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography

Method: X-RAY DIFFRACTION D_max: 78.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e2j
deposition_date	2000-05-23
title	The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography
keywords	TRANSFERASE, ADENINE ANALOG, ENZYME-PRODRUG GENE THERAPY, NUCLEOSIDE- BINDING, THYMIDINE KINASE; 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	25.57 Å
rg_electron	24.06 Å
i0	74722600.00
molecular_weight	68001.0 kDa
excluded_volume	85387 Å³
envelope_volume	98360 Å³
shell_volume	32785 Å³
envelope_diameter	79.6 Å
shell_rg	32.44 Å
envelope_rg	24.27 Å
shape_rg	24.06 Å
total_rg	25.00 Å
total_atoms	4773
n_residues	620
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	78.5 Å
rg_real	25.42 Å
rg_real_error	0.37 Å
i0_real	7.4720e+07
i0_real_error	9.7380e+05
rg_reciprocal	25.47 Å
i0_reciprocal	74730000.0000
total_estimate	0.9017
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	32.9 Å
skewness	0.143
kurtosis	-0.428
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	11450000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	THYMIDINE KINASE
formula_weight	35765.1 kDa
ec_number	2.7.1.21
mutation	YES
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4884

MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSANITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEAN

Source

organism	HERPES SIMPLEX VIRUS (TYPE 1/STRAIN 17)
ncbi_taxonomy_id	10299
host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	THYMIDINE
formula_weight	242.2 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	111

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6. Citations (3)

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length_a	113.400 Å
length_b	117.500 Å
length_c	108.600 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.500 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.2120
r_free	0.2730

fit	/app/data/saxs_computation/e2/1e2j/1e2j.fit
pddf	/app/data/pr_computation/e2/1e2j/1e2j.pr.out
profile	/app/data/saxs_computation/e2/1e2j/1e2j.dat

The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography

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