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1dew

CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ABASIC DNA

Method: X-RAY DIFFRACTION D_max: 101.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dew
deposition_date	1999-11-15
title	CRYSTAL STRUCTURE OF HUMAN 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	31.99 Å
rg_electron	31.16 Å
i0	132343000.00
molecular_weight	80281.0 kDa
excluded_volume	95529 Å³
envelope_volume	124630 Å³
shell_volume	33595 Å³
envelope_diameter	104.9 Å
shell_rg	38.00 Å
envelope_rg	30.88 Å
shape_rg	31.11 Å
total_rg	31.82 Å
total_atoms	5590
n_residues	613
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	101.9 Å
rg_real	32.03 Å
rg_real_error	0.76 Å
i0_real	1.3230e+08
i0_real_error	2.0290e+06
rg_reciprocal	32.02 Å
i0_reciprocal	132300000.0000
total_estimate	0.8972
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.6 Å
skewness	0.261
kurtosis	-0.703
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	18810000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.903

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	5'-D(GPCPGPTPCPCP(3DR)PCPGPAPCPGPAPCP*G)-3'
formula_weight	4446.9 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	X,U
atom_count	6034

GCGTCCNCGACGACG

Entity 2 polymer

description	5'-D(GPTPCPGPTPCPGPGPGPGPAPCPGPC)-3'
formula_weight	4337.8 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	Y,V

GTCGTCGGGGACGC

Entity 3 polymer

description	MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE
formula_weight	31481.8 kDa
ec_number	4.2.99.18
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B

EGPALYEDPPDHKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	444

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6. Citations (1)

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length_a	71.221 Å
length_b	72.249 Å
length_c	93.749 Å
angle_alpha	90.00 °
angle_beta	94.29 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.650 Å
resolution_low	20.000 Å
r_factor	0.1951
r_work	0.1950
r_free	0.2860

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

CRYSTAL STRUCTURE OF HUMAN 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 (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)