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12fk

Ancestral Reconstruction of a Homing Endonuclease

Method: X-RAY DIFFRACTION D_max: 88.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	12fk
deposition_date	2026-04-02
last_revision	2026-04-15
title	Ancestral Reconstruction of a Homing Endonuclease
keywords	Reconstruction, Evolution, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	24.47 Å
rg_electron	23.63 Å
i0	53796300.00
molecular_weight	48850.0 kDa
excluded_volume	57529 Å³
envelope_volume	69592 Å³
shell_volume	25314 Å³
envelope_diameter	91.0 Å
shell_rg	30.31 Å
envelope_rg	24.08 Å
shape_rg	23.56 Å
total_rg	24.46 Å
total_atoms	3381
n_residues	346
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	88.1 Å
rg_real	24.65 Å
rg_real_error	0.87 Å
i0_real	5.3800e+07
i0_real_error	8.3350e+05
rg_reciprocal	24.61 Å
i0_reciprocal	53790000.0000
total_estimate	0.8175
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.2 Å
skewness	0.578
kurtosis	-0.048
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	8993000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.633; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.743; Smooth: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	aHE31
formula_weight	34917.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3694

MGFNSSTNVNPWFWSGLIDAEGSFSIIIDKNKTRKLGWRVQLKFQIGLHTRDLNLLYQLQQYLGGIGSIHIARNRNRVNYSIDSIKDLTKLIIHLDKYPLLTQKAADFLLFKQAVELINNKAHLTIEGLNQIVNIKASMNLGLSDMLKSEFNGYTPVERPVINTDNVIPDPHWISGFVSGEGNFDVRITQTTTKLGYRVQLRFRITQHSRDLKLMEIIVQYLGSGKIYKYPPGKSAVSLTIVNFSDITNIIIPFFNENPILGVKLYDYLDWCKIHELMVNGSHLTVEGINSIREIKSGMNTGRKFD

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 2 polymer

description	;DNA (5'-D(PGPAPAPCPCPTPTPTPGPGPTPTPAPTPGPAPGPGPAPTPCPTPTPC)-3') ;
formula_weight	7390.8 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

GAACCTTTGGTTATGAGGATCTTC

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	synthetic construct

Entity 3 polymer

description	;DNA (5'-D(PTPGPAPAPGPAPTPCPCPTPCPAPTPAPAPCPCPAPAPAPGPGPTPT)-3') ;
formula_weight	7346.8 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

CGAAGATCCTCATAACCAAAGGTT

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	synthetic construct

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	301

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6. Citations (1)

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length_a	58.453 Å
length_b	47.371 Å
length_c	74.737 Å
angle_alpha	90.00 °
angle_beta	98.65 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.170 Å
resolution_low	42.520 Å
r_factor	0.2363
r_work	0.2307
r_free	0.2865

fit	/app/data/saxs_computation/2f/12fk/12fk.fit
pddf	/app/data/pr_computation/2f/12fk/12fk.pr.out
profile	/app/data/saxs_computation/2f/12fk/12fk.dat

Ancestral Reconstruction of a Homing Endonuclease

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

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)