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1dmu

Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence

Method: X-RAY DIFFRACTION D_max: 69.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dmu
deposition_date	1999-12-15
title	Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence
keywords	PROTEIN-DNA COMPLEX, ACTIVE SITE CALCIUM IONS, ALPHA/BETA STRUCTURE, A:A MISMATCH, 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	22.77 Å
rg_electron	21.32 Å
i0	29484700.00
molecular_weight	38930.0 kDa
excluded_volume	47491 Å³
envelope_volume	60040 Å³
shell_volume	23468 Å³
envelope_diameter	70.5 Å
shell_rg	28.17 Å
envelope_rg	21.77 Å
shape_rg	21.28 Å
total_rg	22.23 Å
total_atoms	2714
n_residues	316
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	69.5 Å
rg_real	22.68 Å
rg_real_error	0.37 Å
i0_real	2.9480e+07
i0_real_error	3.4240e+05
rg_reciprocal	22.70 Å
i0_reciprocal	29490000.0000
total_estimate	0.9122
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	27.4 Å
skewness	0.190
kurtosis	-0.512
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	3725000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.981

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;DNA (5'-D(APTPCPGPCPCPTPAPAPTPAPGPGPCPGPAP*T)-3') ;
formula_weight	5211.4 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	F
atom_count	2969

ATCGCCTAATAGGCGAT

Entity 2 polymer

description	BGLI RESTRICTION ENDONUCLEASE
formula_weight	34050.8 kDa
ec_number	3.1.21.4
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MYNLHREKIFMSYNQNKQYLEDNPEIQEKIELYGLNLLNEVISDNEEEIRADYNEANFLHPFWMNYPPLDRGKMPKGDQIPWIEVGEKAVGSKLTRLVSQREDITVREIGLPTGPDERYLLTSPTIYSLTNGFTDSIMMFVDIKSVGPRDSDYDLVLSPNQVSGNGDWAQLEGGIQNNQQTIQGPRSSQIFLPTIPPLYILSDGTIAPVVHLFIKPIYAMRSLTKGDTGQSLYKIKLASVPNGLGLFCNPGYAFDSAYKFLFRPGKDDRTKSLLQKRVRVDLRVLDKIGPRVMTIDMDK

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	4

Entity 4 non-polymer

description	BETA-MERCAPTOETHANOL
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	255

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6. Citations (2)

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length_a	78.480 Å
length_b	81.600 Å
length_c	117.060 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.200 Å
resolution_low	10.000 Å
r_factor	0.1830
r_work	0.1770
r_free	0.2390

fit	/app/data/saxs_computation/dm/1dmu/1dmu.fit
pddf	/app/data/pr_computation/dm/1dmu/1dmu.pr.out
profile	/app/data/saxs_computation/dm/1dmu/1dmu.dat

Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence

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

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)