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1db1

CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMPLEXED TO VITAMIN D

Method: X-RAY DIFFRACTION D_max: 65.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1db1
deposition_date	1999-11-02
title	CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMPLEXED TO VITAMIN D
keywords	COMPLEX, GENE REGULATION; GENE REGULATION
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	19.79 Å
rg_electron	18.59 Å
i0	13962700.00
molecular_weight	28825.0 kDa
excluded_volume	36498 Å³
envelope_volume	41845 Å³
shell_volume	18957 Å³
envelope_diameter	68.5 Å
shell_rg	24.80 Å
envelope_rg	18.95 Å
shape_rg	18.56 Å
total_rg	19.62 Å
total_atoms	2022
n_residues	250
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	65.9 Å
rg_real	19.73 Å
rg_real_error	0.47 Å
i0_real	1.3960e+07
i0_real_error	1.7480e+05
rg_reciprocal	19.74 Å
i0_reciprocal	13960000.0000
total_estimate	0.7912
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	25.1 Å
skewness	0.309
kurtosis	-0.212
angular_range	— – 0.4000 Å⁻¹
current_alpha	0.0000
highest_alpha	2745000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	VITAMIN D NUCLEAR RECEPTOR
formula_weight	29391.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2186

DSLRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFGNEIS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL
formula_weight	416.6 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	164

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6. Citations (1)

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length_a	45.193 Å
length_b	52.443 Å
length_c	133.286 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.800 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.1910
r_free	0.2140

fit	/app/data/saxs_computation/db/1db1/1db1.fit
pddf	/app/data/pr_computation/db/1db1/1db1.pr.out
profile	/app/data/saxs_computation/db/1db1/1db1.dat

CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMPLEXED TO VITAMIN D

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