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1d02

CRYSTAL STRUCTURE OF MUNI RESTRICTION ENDONUCLEASE IN COMPLEX WITH COGNATE DNA

Method: X-RAY DIFFRACTION D_max: 79.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d02
deposition_date	1999-09-08
title	CRYSTAL STRUCTURE OF MUNI RESTRICTION ENDONUCLEASE IN COMPLEX WITH COGNATE DNA
keywords	ALPHA/BETA PROTEIN, PROTEIN-DNA COMPLEX, DISTORTED DOUBLE HELIX, 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	23.53 Å
rg_electron	22.68 Å
i0	49450700.00
molecular_weight	52038.0 kDa
excluded_volume	63906 Å³
envelope_volume	74572 Å³
shell_volume	27212 Å³
envelope_diameter	83.2 Å
shell_rg	30.10 Å
envelope_rg	23.00 Å
shape_rg	22.66 Å
total_rg	23.56 Å
total_atoms	3666
n_residues	417
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	79.7 Å
rg_real	23.48 Å
rg_real_error	0.54 Å
i0_real	4.9450e+07
i0_real_error	6.7330e+05
rg_reciprocal	23.49 Å
i0_reciprocal	49450000.0000
total_estimate	0.7895
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	29.9 Å
skewness	0.350
kurtosis	-0.072
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	11550000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.756; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	;DNA (5'-D(GPCPCPAPAPTPTPGPGPC)-3') ;
formula_weight	3045.0 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	C,D
atom_count	4312

GCCAATTGGC

Entity 2 polymer

description	TYPE II RESTRICTION ENZYME MUNI
formula_weight	23376.5 kDa
ec_number	3.1.21.4
mutation	D83A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B

MGKSELSGRLNWQALAGLKASGAEQNLYNVFNAVFEGTKYVLYEKPKHLKNLYAQVVLPDDVIKEIFNPLIDLSTTQWGVSPAFAIENTETHKILFGEIKRQDGWVEGKDPSAGRGNAHERSCKLFTPGLLKAYRTIGGINDEEILPFWVVFEGDITRDPKRVREITFWYDHYQDNYFMWRPNESGEKLVQHFNEKLKKYLD

Source

organism	Mycoplasma
ncbi_taxonomy_id	2093
host_organism	Escherichia coli

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	646

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6. Citations (1)

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length_a	58.400 Å
length_b	72.470 Å
length_c	121.670 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	1.700 Å
resolution_low	8.000 Å
r_factor	0.1800
r_work	0.1800
r_free	0.2130

fit	/app/data/saxs_computation/d0/1d02/1d02.fit
pddf	/app/data/pr_computation/d0/1d02/1d02.pr.out
profile	/app/data/saxs_computation/d0/1d02/1d02.dat

CRYSTAL STRUCTURE OF MUNI RESTRICTION ENDONUCLEASE IN COMPLEX WITH COGNATE 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 (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Source

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)