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1dnk

THE X-RAY STRUCTURE OF THE DNASE I-D(GGTATACC)2 COMPLEX AT 2.3 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION D_max: 61.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dnk
deposition_date	1992-08-10
title	THE X-RAY STRUCTURE OF THE DNASE I-D(GGTATACC)2 COMPLEX AT 2.3 ANGSTROMS RESOLUTION
keywords	PROTEIN-DNA COMPLEX, DOUBLE HELIX, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
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	19.61 Å
rg_electron	18.17 Å
i0	21613400.00
molecular_weight	33014.0 kDa
excluded_volume	40185 Å³
envelope_volume	45169 Å³
shell_volume	20389 Å³
envelope_diameter	62.2 Å
shell_rg	24.97 Å
envelope_rg	18.41 Å
shape_rg	18.13 Å
total_rg	19.14 Å
total_atoms	2313
n_residues	265
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	61.5 Å
rg_real	19.47 Å
rg_real_error	0.36 Å
i0_real	2.1610e+07
i0_real_error	2.7450e+05
rg_reciprocal	19.49 Å
i0_reciprocal	21610000.0000
total_estimate	0.8215
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.1 Å
skewness	0.141
kurtosis	-0.422
angular_range	— – 0.4050 Å⁻¹
current_alpha	0.0000
highest_alpha	3358000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;DNA (5'-D(GPGPTPAPTPAP*C)-3') ;
formula_weight	2137.4 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B
atom_count	2390

GGTATAC

Entity 2 polymer

description	;DNA (5'-D(GPGPTPAPTPAPCPC)-3') ;
formula_weight	2426.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

GGTATACC

Entity 3 polymer

description	PROTEIN (DEOXYRIBONUCLEASE I (DNASE I) (E.C.3.1.21.1))
formula_weight	29092.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSFSREPAVVKFSSHSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQWSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	77

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6. Citations (8)

X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution.

J.Mol.Biol. (1992)

PMID: 1518054 · DOI: 10.1016/0022-2836(92)91064-V PRIMARY

DNAse I induced DNA conformation: 2 Angstroms structure of a DNAse-octamer complex

J.Mol.Biol. (1991)

Structure refined to 2 Angstroms of a nicked DNA octanucleotide complex with DNAse I

Nature (1988)

Structure of DNase I at 2.0 Angstroms resolution suggests a mechanism for binding to and cutting DNA

Nature (1986)

Crystallographic refinement and structure of DNAse I at 2 Angstroms resolution

J.Mol.Biol. (1986)

Three-dimensional structure of bovine pancreatic DNAse I at 2.5 Angstroms resolution

Embo J. (1984)

Crystallization and preliminary crystallographic data of bovine pancreatic deoxyribonuclease I

J.Mol.Biol. (1982)

Bovine pancreatic deoxyribonuclease A. Isolation of cyanogen bromide peptides, complete covalent structure of the polypeptide chain

J.Biol.Chem. (1973)

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length_a	51.100 Å
length_b	108.400 Å
length_c	62.100 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	2.300 Å
resolution_low	6.000 Å
r_factor	0.1880
r_work	—
r_free	—

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

THE X-RAY STRUCTURE OF THE DNASE I-D(GGTATACC)2 COMPLEX AT 2.3 ANGSTROMS RESOLUTION

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 branched

Entity 5 water

6. Citations (8)

7. Files & Curves (10)

Files (7)

Curves (3)