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1diz

CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA

Method: X-RAY DIFFRACTION D_max: 112.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1diz
deposition_date	1999-11-30
title	CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA
keywords	3-METHYLADENINE DNA GLYCOSYLASE, ALKA, HELIX-HAIRPIN-HELIX, PROTEIN-DNA COMPLEX, 1-AZARIBOSE, HYDROLASE-DNA COMPLEX; HYDROLASE/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	30.70 Å
rg_electron	28.48 Å
i0	118840000.00
molecular_weight	77981.0 kDa
excluded_volume	93918 Å³
envelope_volume	120520 Å³
shell_volume	35727 Å³
envelope_diameter	116.7 Å
shell_rg	35.01 Å
envelope_rg	28.98 Å
shape_rg	28.40 Å
total_rg	29.27 Å
total_atoms	5436
n_residues	614
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	112.0 Å
rg_real	30.81 Å
rg_real_error	1.09 Å
i0_real	1.1880e+08
i0_real_error	1.8740e+06
rg_reciprocal	30.76 Å
i0_reciprocal	118800000.0000
total_estimate	0.8358
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.5 Å
skewness	0.476
kurtosis	-0.123
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	15190000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.688; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.858; Smooth: 0.940

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;DNA (5'-D(GPAPCPAPTPGPAP(NRI)PTPGPCPCP*T)-3') ;
formula_weight	3841.5 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	C,E
atom_count	5643

GACATGAXTGCCT

Entity 2 polymer

description	;DNA (5'-D(GPGPCPAPAPTPCPAPTPGPTPCP*A)-3') ;
formula_weight	3975.6 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	D,F

GGCAATCATGTCA

Entity 3 polymer

description	3-METHYLADENINE DNA GLYCOSYLASE II
formula_weight	31425.2 kDa
ec_number	3.2.2.21
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B

MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	207

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6. Citations (1)

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length_a	82.400 Å
length_b	82.400 Å
length_c	199.700 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 31 2 1
int_tables_number	152
crystal_system	—

resolution	2.500 Å
resolution_low	10.000 Å
r_factor	0.2500
r_work	0.2500
r_free	0.2900

fit	/app/data/saxs_computation/di/1diz/1diz.fit
pddf	/app/data/pr_computation/di/1diz/1diz.pr.out
profile	/app/data/saxs_computation/di/1diz/1diz.dat

CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH 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)