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1de8

HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA

Method: X-RAY DIFFRACTION D_max: 100.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1de8
deposition_date	1999-11-13
title	HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA
keywords	ENZYME:DNA COMPLEX, DNA REPAIR, ABASIC SITE, LYASE-DNA COMPLEX; LYASE/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	31.91 Å
rg_electron	31.56 Å
i0	109174000.00
molecular_weight	75364.0 kDa
excluded_volume	90854 Å³
envelope_volume	115040 Å³
shell_volume	30742 Å³
envelope_diameter	99.8 Å
shell_rg	37.91 Å
envelope_rg	31.31 Å
shape_rg	31.55 Å
total_rg	32.07 Å
total_atoms	5264
n_residues	594
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	100.9 Å
rg_real	32.03 Å
rg_real_error	0.88 Å
i0_real	1.0920e+08
i0_real_error	1.8780e+06
rg_reciprocal	31.98 Å
i0_reciprocal	109200000.0000
total_estimate	0.8682
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.2 Å
skewness	0.292
kurtosis	-0.841
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	24250000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.880; Smooth: 0.932

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	;DNA (5'-D(GPCPTPAPCP(3DR)PGPAPTPCP*G)-3') ;
formula_weight	3225.1 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	X,U
atom_count	5308

GCTACNGATCG

Entity 2 polymer

description	;DNA (5'-D(CPGPAPTPCPGPGPTPAPGP*C)-3') ;
formula_weight	3374.2 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	Y,V

CGATCGGTAGC

Entity 3 polymer

description	MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE
formula_weight	31198.6 kDa
ec_number	4.2.99.18
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A

ALYEDPPDHKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	44

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6. Citations (1)

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length_a	122.850 Å
length_b	122.850 Å
length_c	107.070 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 41
int_tables_number	80
crystal_system	—

resolution	2.950 Å
resolution_low	20.000 Å
r_factor	0.1900
r_work	0.1900
r_free	0.3120

fit	/app/data/saxs_computation/de/1de8/1de8.fit
pddf	/app/data/pr_computation/de/1de8/1de8.pr.out
profile	/app/data/saxs_computation/de/1de8/1de8.dat

HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA

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)