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1ebm

CRYSTAL STRUCTURE OF THE HUMAN 8-OXOGUANINE GLYCOSYLASE (HOGG1) BOUND TO A SUBSTRATE OLIGONUCLEOTIDE

Method: X-RAY DIFFRACTION D_max: 73.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ebm
deposition_date	2000-01-24
title	CRYSTAL STRUCTURE OF THE HUMAN 8-OXOGUANINE GLYCOSYLASE (HOGG1) BOUND TO A SUBSTRATE OLIGONUCLEOTIDE
keywords	DNA repair, DNA glycosylase, protein/DNA, 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	22.65 Å
rg_electron	21.37 Å
i0	41842500.00
molecular_weight	43760.0 kDa
excluded_volume	51963 Å³
envelope_volume	63449 Å³
shell_volume	24585 Å³
envelope_diameter	74.6 Å
shell_rg	28.54 Å
envelope_rg	21.58 Å
shape_rg	21.34 Å
total_rg	22.22 Å
total_atoms	3050
n_residues	343
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	73.6 Å
rg_real	22.55 Å
rg_real_error	0.43 Å
i0_real	4.1840e+07
i0_real_error	5.6390e+05
rg_reciprocal	22.57 Å
i0_reciprocal	41840000.0000
total_estimate	0.7173
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	29.0 Å
skewness	0.197
kurtosis	-0.367
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	5438000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.997; Smooth: 0.993

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;DNA (5'-D(GPCPGPTPCPCPAP(8OG)PGPTPCPTPAPCP*C)-3') ;
formula_weight	4561.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C
atom_count	3183

GCGTCCAGGTCTACC

Entity 2 polymer

description	;DNA (5'-D(GPGPTPAPGPAPCPCPTPGPGPAPCPGP*C)-3') ;
formula_weight	4635.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

GGTAGACCTGGACGC

Entity 3 polymer

description	8-OXOGUANINE DNA GLYCOSYLASE
formula_weight	35647.3 kDa
mutation	K249Q
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

GSEGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTQVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADLRQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	133

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6. Citations (1)

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length_a	92.357 Å
length_b	92.357 Å
length_c	212.872 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65 2 2
int_tables_number	179
crystal_system	—

resolution	2.100 Å
resolution_low	25.000 Å
r_factor	0.2350
r_work	0.2320
r_free	0.2630

fit	/app/data/saxs_computation/eb/1ebm/1ebm.fit
pddf	/app/data/pr_computation/eb/1ebm/1ebm.pr.out
profile	/app/data/saxs_computation/eb/1ebm/1ebm.dat

CRYSTAL STRUCTURE OF THE HUMAN 8-OXOGUANINE GLYCOSYLASE (HOGG1) BOUND TO A SUBSTRATE OLIGONUCLEOTIDE

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)