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1d3y

STRUCTURE OF THE DNA TOPOISOMERASE VI A SUBUNIT

Method: X-RAY DIFFRACTION D_max: 79.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d3y
deposition_date	1999-10-01
title	STRUCTURE OF THE DNA TOPOISOMERASE VI A SUBUNIT
keywords	TOPOISOMERASE VI, DNA BINDING PROTEIN, SPO11 HOMOLOG, ISOMERASE; ISOMERASE
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	25.77 Å
rg_electron	24.68 Å
i0	67738600.00
molecular_weight	65967.0 kDa
excluded_volume	83227 Å³
envelope_volume	99008 Å³
shell_volume	32129 Å³
envelope_diameter	80.1 Å
shell_rg	33.13 Å
envelope_rg	24.63 Å
shape_rg	24.67 Å
total_rg	25.60 Å
total_atoms	4653
n_residues	579
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	79.2 Å
rg_real	25.60 Å
rg_real_error	0.42 Å
i0_real	6.7740e+07
i0_real_error	8.5300e+05
rg_reciprocal	25.66 Å
i0_reciprocal	67740000.0000
total_estimate	0.9058
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.5 Å
skewness	0.074
kurtosis	-0.578
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	31560000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DNA TOPOISOMERASE VI A SUBUNIT
formula_weight	34098.8 kDa
ec_number	5.99.1.3
mutation	DELETED NONCONSERVED N-TERMINAL RESIDUES 1-69
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4979

TVNQAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEAALGVLREHLGFIPEEDGSSVVGPLKIIEETPEGELVVDCTKLGTGAYNIPNDVTKLNLETDADFILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRLHEEHDLPVLVFTDGDPYGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDIIDYDLPTHPLKEQDIKRIKDGLKNDDFVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIKDESTWLP

Source

organism	Methanocaldococcus jannaschii
ncbi_taxonomy_id	2190
host_organism	Escherichia coli

Entity 2 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	326

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6. Citations (1)

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length_a	66.510 Å
length_b	59.040 Å
length_c	87.260 Å
angle_alpha	90.00 °
angle_beta	94.05 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.000 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.1970
r_free	0.2420

fit	/app/data/saxs_computation/d3/1d3y/1d3y.fit
pddf	/app/data/pr_computation/d3/1d3y/1d3y.pr.out
profile	/app/data/saxs_computation/d3/1d3y/1d3y.dat

STRUCTURE OF THE DNA TOPOISOMERASE VI A SUBUNIT

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