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9vkn

Crystal structure of DhdR in complex with inducer L2HG

Method: X-RAY DIFFRACTION D_max: 73.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vkn
deposition_date	2025-06-23
title	Crystal structure of DhdR in complex with inducer L2HG
keywords	Transcriptional regulator, 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	20.64 Å
rg_electron	19.73 Å
i0	18616100.00
molecular_weight	31037.0 kDa
excluded_volume	38182 Å³
envelope_volume	44350 Å³
shell_volume	19285 Å³
envelope_diameter	73.4 Å
shell_rg	25.60 Å
envelope_rg	19.92 Å
shape_rg	19.74 Å
total_rg	20.47 Å
total_atoms	2178
n_residues	290
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	73.0 Å
rg_real	20.65 Å
rg_real_error	0.57 Å
i0_real	1.8620e+07
i0_real_error	2.5990e+05
rg_reciprocal	20.65 Å
i0_reciprocal	18620000.0000
total_estimate	0.8569
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.3 Å
skewness	0.401
kurtosis	-0.212
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	6034000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.741; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.929; Smooth: 0.985

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Pyruvate dehydrogenase complex repressor
formula_weight	16437.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2206

VSAGLDDREQLASVYELRMELEGGAAALAARRRNATDLAAMAEALAALEANLDHPEQGVEHDIAFHVAIAAATHNRYYQDLLQYLNLQLRLAVSTARTNSRRQEGLTAVVHQEHVAVYDAILAGDPDRARLAATRHLQQAASRLRLDLLS

Source

organism	Achromobacter denitrificans
ncbi_taxonomy_id	32002
host_organism	Escherichia coli

Entity 2 non-polymer

description	(2S)-2-HYDROXYPENTANEDIOIC ACID
formula_weight	148.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	28

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6. Citations (1)

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length_a	126.984 Å
length_b	126.984 Å
length_c	39.776 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 41 21 2
int_tables_number	92
crystal_system	tetragonal

resolution	2.440 Å
resolution_low	24.810 Å
r_factor	0.2003
r_work	0.1981
r_free	0.2396

fit	/app/data/saxs_computation/vk/9vkn/9vkn.fit
pddf	/app/data/pr_computation/vk/9vkn/9vkn.pr.out
profile	/app/data/saxs_computation/vk/9vkn/9vkn.dat