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1de9

HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION

Method: X-RAY DIFFRACTION D_max: 129.2 Å Quality: SUSPICIOUS

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1de9
deposition_date	1999-11-13
title	HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION
keywords	ENZYME:DNA COMPLEX, DNA REPAIR ABASIC SITE, AP ENDONUCLEASE, 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	39.76 Å
rg_electron	39.21 Å
i0	93946200.00
molecular_weight	72792.0 kDa
excluded_volume	88287 Å³
envelope_volume	119260 Å³
shell_volume	25143 Å³
envelope_diameter	130.4 Å
shell_rg	45.79 Å
envelope_rg	37.92 Å
shape_rg	39.18 Å
total_rg	39.64 Å
total_atoms	5088
n_residues	586
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	129.2 Å
rg_real	40.30 Å
rg_real_error	1.40 Å
i0_real	9.3950e+07
i0_real_error	1.6130e+06
rg_reciprocal	39.99 Å
i0_reciprocal	93910000.0000
total_estimate	0.4019
solution_quality	SUSPICIOUS a SUSPICIOUS solution
n_peaks	2
r_peak_primary	25.8 Å
skewness	0.264
kurtosis	-1.193
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	17640000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.048; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.133; Smooth: 0.756

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	5'-d(CPTPAPC)-3'
formula_weight	1150.8 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	X,U
atom_count	5088

CTAC

Entity 2 polymer

description	5'-d(P(3DR)PGPAPTP*C)-3'
formula_weight	1370.9 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	Y,V

NGATC

Entity 3 polymer

description	5'-d(GPAPTPCPGPGPTPAP*G)-3'
formula_weight	2795.8 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	Z,W

GATCGGTAG

Entity 4 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	A,B

ALYEDPPDHKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	90.060 Å
length_b	98.350 Å
length_c	101.050 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	3.000 Å
resolution_low	20.000 Å
r_factor	0.1831
r_work	0.1830
r_free	0.2740

fit	/app/data/saxs_computation/de/1de9/1de9.fit
pddf	/app/data/pr_computation/de/1de9/1de9.pr.out
profile	/app/data/saxs_computation/de/1de9/1de9.dat

HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION

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 (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)