← Back to search

1cy7

;COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE ;

Method: X-RAY DIFFRACTION D_max: 101.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1cy7
deposition_date	1999-08-31
title	;COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE ;
keywords	DNA TOPOISOMERASE, RELAXING ENZYME, ISOMERASE; ISOMERASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	30.28 Å
rg_electron	30.01 Å
i0	71475700.00
molecular_weight	64767.0 kDa
excluded_volume	80494 Å³
envelope_volume	108560 Å³
shell_volume	31583 Å³
envelope_diameter	106.1 Å
shell_rg	35.37 Å
envelope_rg	30.05 Å
shape_rg	30.02 Å
total_rg	30.48 Å
total_atoms	4553
n_residues	563
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

▼

3. P(r) Analysis (GNOM)

dmax	101.5 Å
rg_real	30.39 Å
rg_real_error	0.85 Å
i0_real	7.1480e+07
i0_real_error	1.0610e+06
rg_reciprocal	30.34 Å
i0_reciprocal	71470000.0000
total_estimate	0.8792
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.2 Å
skewness	0.414
kurtosis	-0.353
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	12010000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.873

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	DNA TOPOISOMERASE I
formula_weight	67542.5 kDa
ec_number	5.99.1.2
mutation	GLY-SER ATTACHED AT N-TERMINUS DUE TO CONSTRUCT
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4680

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	1

Entity 3 non-polymer

description	THYMIDINE-5'-PHOSPHATE
formula_weight	322.2 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	127

▶

6. Citations (1)

▶

length_a	63.830 Å
length_b	79.370 Å
length_c	141.700 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	2.400 Å
resolution_low	19.840 Å
r_factor	0.2340
r_work	0.2340
r_free	0.2950

fit	/app/data/saxs_computation/cy/1cy7/1cy7.fit
pddf	/app/data/pr_computation/cy/1cy7/1cy7.pr.out
profile	/app/data/saxs_computation/cy/1cy7/1cy7.dat

;COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE ;

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