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1dgm

CRYSTAL STRUCTURE OF ADENOSINE KINASE FROM TOXOPLASMA GONDII

Method: X-RAY DIFFRACTION D_max: 66.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dgm
deposition_date	1999-11-24
title	CRYSTAL STRUCTURE OF ADENOSINE KINASE FROM TOXOPLASMA GONDII
keywords	TOXOPLASMA GONDII, ADENOSINE KINASE, PURINE METABOLISM, 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	20.80 Å
rg_electron	19.69 Å
i0	23509900.00
molecular_weight	37136.0 kDa
excluded_volume	46527 Å³
envelope_volume	53863 Å³
shell_volume	22398 Å³
envelope_diameter	67.5 Å
shell_rg	26.56 Å
envelope_rg	19.94 Å
shape_rg	19.70 Å
total_rg	20.56 Å
total_atoms	2605
n_residues	346
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	66.5 Å
rg_real	20.68 Å
rg_real_error	0.38 Å
i0_real	2.3510e+07
i0_real_error	3.3800e+05
rg_reciprocal	20.71 Å
i0_reciprocal	23510000.0000
total_estimate	0.8923
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.0 Å
skewness	0.190
kurtosis	-0.375
angular_range	— – 0.3800 Å⁻¹
current_alpha	0.0000
highest_alpha	5624000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.979

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	ADENOSINE KINASE
formula_weight	38424.8 kDa
ec_number	2.7.1.20
mutation	L179F
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2752

MAVDSSNSATGPMRVFAIGNPILDLVAEVPSSFLDEFFLKRGDATLATPEQMRIYSTLDQFNPTSLPGGSALNSVRVVQKLLRKPGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMVAPGQSTGVCAVLINEKERTLCTHLGACGSFRLPEDWTTFASGALIFYATAYTLTATPKNAFEVAGYAHGIPNAIFTLNLSAPFCVELYKDAMQSLLLHTNILFGNEEEFAHLAKVHNLVAAEKTALSTANKEHAVEVCTGALRLLTAGQNTGATKLVVMTRGHNPVIAAEQTADGTVVVHEVGVPVVAAEKIVDTNGAGDAFVGGFLYALSQGKTVKQCIMCGNACAQDVIQHVGFSLSFTSLPC

Source

organism	Toxoplasma gondii
ncbi_taxonomy_id	5811
host_organism	Escherichia coli

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	ADENOSINE
formula_weight	267.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	ACETIC ACID
formula_weight	60.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	142

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6. Citations (1)

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length_a	47.550 Å
length_b	68.750 Å
length_c	57.290 Å
angle_alpha	90.00 °
angle_beta	100.30 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.800 Å
resolution_low	46.780 Å
r_factor	0.2140
r_work	0.2140
r_free	0.2330

fit	/app/data/saxs_computation/dg/1dgm/1dgm.fit
pddf	/app/data/pr_computation/dg/1dgm/1dgm.pr.out
profile	/app/data/saxs_computation/dg/1dgm/1dgm.dat