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1ekh

NMR STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND COBALT

Method: SOLUTION NMR D_max: 35.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ekh
deposition_date	2000-03-08
title	NMR STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND COBALT
keywords	drug bound in the minor groove of DNA, DNA; DNA
method	SOLUTION NMR

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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	11.08 Å
rg_electron	11.02 Å
i0	50319800.00
molecular_weight	43601.0 kDa
excluded_volume	48026 Å³
envelope_volume	10648 Å³
shell_volume	8079 Å³
envelope_diameter	36.8 Å
shell_rg	16.86 Å
envelope_rg	12.00 Å
shape_rg	10.91 Å
total_rg	11.53 Å
total_atoms	5010
n_residues	96
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	35.4 Å
rg_real	11.05 Å
rg_real_error	0.21 Å
i0_real	5.0320e+07
i0_real_error	5.4030e+05
rg_reciprocal	11.05 Å
i0_reciprocal	50320000.0000
total_estimate	0.7499
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	12.1 Å
skewness	0.200
kurtosis	-0.578
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	117200.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.987; Smooth: 0.890

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;DNA (5'-D(TPTPGPGPCPCPAPA)-3') ;
formula_weight	2426.6 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	A,B
atom_count	5010

TTGGCCAA

Entity 2 branched

description	2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-4-O-acetyl-2,6-dideoxy-beta-D-galactopyranose
formula_weight	334.4 kDa
src_method	man
entity_count	2

Entity 3 branched

description	3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-beta-D-Olivopyranose-(1-3)-beta-D-Olivopyranose
formula_weight	464.5 kDa
src_method	man
entity_count	2

Entity 4 non-polymer

description	COBALT (II) ION
formula_weight	58.9 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	(1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose
formula_weight	420.4 kDa
src_method	syn
entity_count	2

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6. Citations (2)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	1

space_group	P 1
int_tables_number	1
crystal_system	—

fit	/app/data/saxs_computation/ek/1ekh/1ekh.fit
pddf	/app/data/pr_computation/ek/1ekh/1ekh.pr.out
profile	/app/data/saxs_computation/ek/1ekh/1ekh.dat

NMR STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND COBALT

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Entity 2 branched

Entity 3 branched

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)