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1cy4

;COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'pTpTpTp3' ;

Method: X-RAY DIFFRACTION D_max: 102.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1cy4
deposition_date	1999-08-31
title	;COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'pTpTpTp3' ;
keywords	DNA TOPOISOMERASE, RELAXING ENZYME, 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	30.46 Å
rg_electron	30.19 Å
i0	69028500.00
molecular_weight	63727.0 kDa
excluded_volume	79280 Å³
envelope_volume	107710 Å³
shell_volume	31288 Å³
envelope_diameter	105.7 Å
shell_rg	35.36 Å
envelope_rg	30.14 Å
shape_rg	30.21 Å
total_rg	30.64 Å
total_atoms	4480
n_residues	558
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	102.1 Å
rg_real	30.57 Å
rg_real_error	0.82 Å
i0_real	6.9030e+07
i0_real_error	1.1540e+06
rg_reciprocal	30.52 Å
i0_reciprocal	69030000.0000
total_estimate	0.8798
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.4 Å
skewness	0.406
kurtosis	-0.383
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	10950000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.905; Smooth: 0.879

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DNA TOPOISOMERASE I
formula_weight	67542.5 kDa
ec_number	5.99.1.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4758

GSMGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSI

Source

organism	Escherichia coli
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

Entity 2 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	THYMIDINE-5'-PHOSPHATE
formula_weight	322.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	278

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6. Citations (1)

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length_a	63.950 Å
length_b	78.760 Å
length_c	141.710 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.550 Å
resolution_low	19.760 Å
r_factor	0.2210
r_work	0.2210
r_free	0.2990

fit	/app/data/saxs_computation/cy/1cy4/1cy4.fit
pddf	/app/data/pr_computation/cy/1cy4/1cy4.pr.out
profile	/app/data/saxs_computation/cy/1cy4/1cy4.dat

;COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'pTpTpTp3' ;

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