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9w4v

Structure of transcription factor in complex with D-allo-Ile

Method: X-RAY DIFFRACTION D_max: 63.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w4v
deposition_date	2025-08-01
title	Structure of transcription factor in complex with D-allo-Ile
keywords	D-amino acid, amino acid racemase, transcription factor, Pyrococcus horikoshii, TRANSCRIPTION; TRANSCRIPTION
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	21.00 Å
rg_electron	19.83 Å
i0	18216000.00
molecular_weight	33880.0 kDa
excluded_volume	43171 Å³
envelope_volume	49073 Å³
shell_volume	20794 Å³
envelope_diameter	63.1 Å
shell_rg	26.11 Å
envelope_rg	19.92 Å
shape_rg	19.79 Å
total_rg	20.81 Å
total_atoms	2382
n_residues	294
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	63.0 Å
rg_real	20.88 Å
rg_real_error	0.34 Å
i0_real	1.8220e+07
i0_real_error	2.2350e+05
rg_reciprocal	20.90 Å
i0_reciprocal	18220000.0000
total_estimate	0.9127
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	27.4 Å
skewness	0.125
kurtosis	-0.544
angular_range	— – 0.3800 Å⁻¹
current_alpha	0.0000
highest_alpha	5452000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Uncharacterized HTH-type transcriptional regulator PH0140
formula_weight	20126.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2437

MGSSHHHHHHSSGLVPRGSHMITVPHSRKVELDEIDRAILRLLQEDGRMSYSEISRRINVPESTVRARVNRLVKEGVIRKFAALINPFKAGYEIVAFIAVDAEPAKVKQVVEELAKFPEVDVLGIVTGAHDIFMQVTVKDLQELERFILEKMAKIDGIKSTETSILTSVKKWGYARVF

Source

organism	Pyrococcus horikoshii
ncbi_taxonomy_id	53953
host_organism	Escherichia coli

Entity 2 non-polymer

description	D-alloisoleucine
formula_weight	131.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	55

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6. Citations (1)

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length_a	68.250 Å
length_b	102.147 Å
length_c	102.485 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 2 2 2
int_tables_number	23
crystal_system	—

resolution	2.300 Å
resolution_low	30.570 Å
r_factor	0.2109
r_work	0.2075
r_free	0.2705

fit	/app/data/saxs_computation/w4/9w4v/9w4v.fit
pddf	/app/data/pr_computation/w4/9w4v/9w4v.pr.out
profile	/app/data/saxs_computation/w4/9w4v/9w4v.dat