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1dna

D221(169)N MUTANT DOES NOT PROMOTE OPENING OF THE COFACTOR IMIDAZOLIDINE RING

Method: X-RAY DIFFRACTION D_max: 73.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dna
deposition_date	1998-06-25
title	D221(169)N MUTANT DOES NOT PROMOTE OPENING OF THE COFACTOR IMIDAZOLIDINE RING
keywords	TRANSFERASE, ACTIVE SITE MUTANT, REACTION INTERMEDIATE, METHYLTRANSFERASE; 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	24.32 Å
rg_electron	23.02 Å
i0	65040400.00
molecular_weight	62601.0 kDa
excluded_volume	78021 Å³
envelope_volume	88614 Å³
shell_volume	30830 Å³
envelope_diameter	73.7 Å
shell_rg	31.25 Å
envelope_rg	23.25 Å
shape_rg	23.02 Å
total_rg	23.92 Å
total_atoms	4416
n_residues	526
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	73.5 Å
rg_real	24.16 Å
rg_real_error	0.30 Å
i0_real	6.5040e+07
i0_real_error	7.4230e+05
rg_reciprocal	24.20 Å
i0_reciprocal	65040000.0000
total_estimate	0.7341
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	31.5 Å
skewness	0.182
kurtosis	-0.400
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	15570000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 0.264; Positv: 1.000; Valcen: 0.987; Smooth: 0.970

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	THYMIDYLATE SYNTHASE
formula_weight	30558.7 kDa
ec_number	2.1.1.45
mutation	D169N
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4632

MKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCNVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLYSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPVAI

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 non-polymer

description	;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ;
formula_weight	308.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	10-PROPARGYL-5,8-DIDEAZAFOLIC ACID
formula_weight	477.5 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	216

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6. Citations (3)

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length_a	127.221 Å
length_b	127.221 Å
length_c	68.178 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 63
int_tables_number	173
crystal_system	—

resolution	2.200 Å
resolution_low	7.000 Å
r_factor	0.1800
r_work	0.1800
r_free	0.2260

fit	/app/data/saxs_computation/dn/1dna/1dna.fit
pddf	/app/data/pr_computation/dn/1dna/1dna.pr.out
profile	/app/data/saxs_computation/dn/1dna/1dna.dat

D221(169)N MUTANT DOES NOT PROMOTE OPENING OF THE COFACTOR IMIDAZOLIDINE RING

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