← Back to search

9w4w

Structure of transcription factor in complex with L-Ile

Method: X-RAY DIFFRACTION D_max: 63.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9w4w
deposition_date	2025-08-01
title	Structure of transcription factor in complex with L-Ile
keywords	D-amino acid, amino acid racemase, transcription factor, Pyrococcus horikoshii, TRANSCRIPTION; TRANSCRIPTION
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	20.48 Å
rg_electron	19.52 Å
i0	5206990.00
molecular_weight	17201.0 kDa
excluded_volume	21845 Å³
envelope_volume	27826 Å³
shell_volume	12981 Å³
envelope_diameter	64.8 Å
shell_rg	23.97 Å
envelope_rg	19.11 Å
shape_rg	19.48 Å
total_rg	20.39 Å
total_atoms	1208
n_residues	149
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

▼

3. P(r) Analysis (GNOM)

dmax	63.9 Å
rg_real	20.54 Å
rg_real_error	0.47 Å
i0_real	5.2070e+06
i0_real_error	7.0680e+04
rg_reciprocal	20.53 Å
i0_reciprocal	5207000.0000
total_estimate	0.8468
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	17.3 Å
skewness	0.287
kurtosis	-0.716
angular_range	— – 0.3900 Å⁻¹
current_alpha	0.0000
highest_alpha	1142000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.897; Smooth: 0.426

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Uncharacterized HTH-type transcriptional regulator PH0140
formula_weight	20126.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1351

MGSSHHHHHHSSGLVPRGSHMITVPHSRKVELDEIDRAILRLLQEDGRMSYSEISRRINVPESTVRARVNRLVKEGVIRKFAALINPFKAGYEIVAFIAVDAEPAKVKQVVEELAKFPEVDVLGIVTGAHDIFMQVTVKDLQELERFILEKMAKIDGIKSTETSILTSVKKWGYARVF

Source

organism	Pyrococcus horikoshii
ncbi_taxonomy_id	53953
host_organism	Escherichia coli

Entity 2 non-polymer

description	ISOLEUCINE
formula_weight	131.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	129

▶

6. Citations (1)

▶

length_a	101.116 Å
length_b	101.116 Å
length_c	70.410 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 4 2 2
int_tables_number	97
crystal_system	—

resolution	1.390 Å
resolution_low	32.000 Å
r_factor	0.1788
r_work	0.1779
r_free	0.1946

fit	/app/data/saxs_computation/w4/9w4w/9w4w.fit
pddf	/app/data/pr_computation/w4/9w4w/9w4w.pr.out
profile	/app/data/saxs_computation/w4/9w4w/9w4w.dat

Structure of transcription factor in complex with L-Ile

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