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1dfm

Crystal structure of restriction endonuclease BGLII complexed with DNA 16-mer

Method: X-RAY DIFFRACTION D_max: 73.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dfm
deposition_date	1999-12-06
title	Crystal structure of restriction endonuclease BGLII complexed with DNA 16-mer
keywords	RESTRICTION ENDONUCLEASE, RESTRICTION ENZYME, PROTEIN-DNA COMPLEX, 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	23.21 Å
rg_electron	22.58 Å
i0	72870500.00
molecular_weight	61236.0 kDa
excluded_volume	73927 Å³
envelope_volume	86397 Å³
shell_volume	30563 Å³
envelope_diameter	74.2 Å
shell_rg	30.88 Å
envelope_rg	22.87 Å
shape_rg	22.58 Å
total_rg	23.39 Å
total_atoms	4242
n_residues	463
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	73.1 Å
rg_real	23.06 Å
rg_real_error	0.44 Å
i0_real	7.2870e+07
i0_real_error	8.9150e+05
rg_reciprocal	23.10 Å
i0_reciprocal	72870000.0000
total_estimate	0.8931
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	29.2 Å
skewness	0.169
kurtosis	-0.402
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	18780000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	;DNA (5'-D(TPAPTPTPAPTPAPGPAPTPCPTPAPTPAPA)-3') ;
formula_weight	4895.2 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	C,D
atom_count	4850

TATTATAGATCTATAA

Entity 2 polymer

description	ENDONUCLEASE BGLII
formula_weight	26031.8 kDa
mutation	SELENOMETHIONYL (MSE FOR MET)
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B

MKIDITDYNHADEILNPQLWKEIEETLLKMPLHVKASDQASKVGSLIFDPVGTNQYIKDELVPKHWKNNIPIPKRFDFLGTDIDFGKRDTLVEVQFSNYPFLLNNTVRSELFHKSNMDIDEEGMKVAIIITKGHMFPASNSSLYYEQAQNQLNSLAEYNVFDVPIRLVGLIEDFETDIDIVSTTYADKRYSRTITKRDTVKGKVIDTNTPNTRRRKRGTIVTY

Source

organism	Bacillus subtilis
ncbi_taxonomy_id	1423
host_organism	Escherichia coli

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	608

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6. Citations (1)

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length_a	48.700 Å
length_b	101.800 Å
length_c	116.900 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	1.500 Å
resolution_low	20.000 Å
r_factor	0.1920
r_work	0.1920
r_free	0.2240

fit	/app/data/saxs_computation/df/1dfm/1dfm.fit
pddf	/app/data/pr_computation/df/1dfm/1dfm.pr.out
profile	/app/data/saxs_computation/df/1dfm/1dfm.dat

Crystal structure of restriction endonuclease BGLII complexed with DNA 16-mer

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

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)