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1e2k

;Kinetics and crystal structure of the wild-type and the engineered Y101F mutant of Herpes simplex virus type 1 thymidine kinase interacting with (North)-methanocarba-thymidine ;

Method: X-RAY DIFFRACTION D_max: 79.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e2k
deposition_date	2000-05-23
title	;Kinetics and crystal structure of the wild-type and the engineered Y101F mutant of Herpes simplex virus type 1 thymidine kinase interacting with (North)-methanocarba-thymidine ;
keywords	TRANSFERASE, THYMIDINE KINASE, ANTIVIRAL DRUG, ENZYME-PRODRUG GENE THERAPY, SUGAR RING PUCKER; 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	25.60 Å
rg_electron	24.08 Å
i0	75141000.00
molecular_weight	68437.0 kDa
excluded_volume	85981 Å³
envelope_volume	98868 Å³
shell_volume	32887 Å³
envelope_diameter	80.6 Å
shell_rg	32.44 Å
envelope_rg	24.31 Å
shape_rg	24.08 Å
total_rg	24.99 Å
total_atoms	4805
n_residues	624
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	79.4 Å
rg_real	25.45 Å
rg_real_error	0.43 Å
i0_real	7.5140e+07
i0_real_error	1.0860e+06
rg_reciprocal	25.50 Å
i0_reciprocal	75140000.0000
total_estimate	0.8991
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.3 Å
skewness	0.147
kurtosis	-0.421
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	12500000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.981

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	THYMIDINE KINASE
formula_weight	35779.1 kDa
ec_number	2.7.1.21
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5169

MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEAN

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	1-[4-HYDROXY-5-(HYDROXYMETHYL)BICYCLO[3.1.0]HEX-2-YL]-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE
formula_weight	252.3 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	364

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6. Citations (3)

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length_a	114.000 Å
length_b	117.700 Å
length_c	108.200 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	1.700 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.2090
r_free	0.2520

fit	/app/data/saxs_computation/e2/1e2k/1e2k.fit
pddf	/app/data/pr_computation/e2/1e2k/1e2k.pr.out
profile	/app/data/saxs_computation/e2/1e2k/1e2k.dat

;Kinetics and crystal structure of the wild-type and the engineered Y101F mutant of Herpes simplex virus type 1 thymidine kinase interacting with (North)-methanocarba-thymidine ;

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