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1ej9

CRYSTAL STRUCTURE OF HUMAN TOPOISOMERASE I DNA COMPLEX

Method: X-RAY DIFFRACTION D_max: 80.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ej9
deposition_date	2000-03-01
title	CRYSTAL STRUCTURE OF HUMAN TOPOISOMERASE I DNA COMPLEX
keywords	protein-dna complex, type I topoisomerase, human, ISOMERASE-DNA COMPLEX; ISOMERASE/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	26.48 Å
rg_electron	26.09 Å
i0	96354900.00
molecular_weight	69773.0 kDa
excluded_volume	84138 Å³
envelope_volume	107130 Å³
shell_volume	33891 Å³
envelope_diameter	84.8 Å
shell_rg	33.72 Å
envelope_rg	26.01 Å
shape_rg	26.09 Å
total_rg	26.78 Å
total_atoms	4862
n_residues	527
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	80.1 Å
rg_real	26.35 Å
rg_real_error	0.51 Å
i0_real	9.6350e+07
i0_real_error	1.3330e+06
rg_reciprocal	26.39 Å
i0_reciprocal	96360000.0000
total_estimate	0.9097
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	77.4 Å
skewness	0.189
kurtosis	-0.464
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	10680000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	;DNA (5'-D(CAPAPAPAPAPGPAPCPTPCPAPGPAPAPAPAPAPTPTPTPTP*T)-3') ;
formula_weight	7064.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C
atom_count	5215

CAAAAAGACTCAGAAAAATTTTT

Entity 2 polymer

description	;DNA (5'-D(CAPAPAPAPAPTPTPTPTPTPCPTPGPAPGPTPCPTPTPTPTP*T)-3') ;
formula_weight	7010.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

CAAAAATTTTTCTGAGTCTTTTT

Entity 3 polymer

description	DNA TOPOISOMERASE I
formula_weight	66593.8 kDa
ec_number	5.99.1.2
mutation	Y723F
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

WKWWEEERYPEGIKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQIAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNFLDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMADEDYEF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	353

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6. Citations (1)

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length_a	56.980 Å
length_b	124.920 Å
length_c	72.290 Å
angle_alpha	90.00 °
angle_beta	93.84 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.600 Å
resolution_low	15.000 Å
r_factor	—
r_work	0.2140
r_free	0.2810

fit	/app/data/saxs_computation/ej/1ej9/1ej9.fit
pddf	/app/data/pr_computation/ej/1ej9/1ej9.pr.out
profile	/app/data/saxs_computation/ej/1ej9/1ej9.dat

CRYSTAL STRUCTURE OF HUMAN TOPOISOMERASE I DNA COMPLEX

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

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)