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9v67

The crystal structure of a ThDP-dependent enzyme PpBFD

Method: X-RAY DIFFRACTION D_max: 113.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v67
deposition_date	2025-05-26
title	The crystal structure of a ThDP-dependent enzyme PpBFD
keywords	thiamine-dependent photobiocatalysis, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC 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	36.63 Å
rg_electron	35.71 Å
i0	761584000.00
molecular_weight	222940.0 kDa
excluded_volume	277700 Å³
envelope_volume	323090 Å³
shell_volume	70458 Å³
envelope_diameter	117.7 Å
shell_rg	45.16 Å
envelope_rg	36.01 Å
shape_rg	35.70 Å
total_rg	36.26 Å
total_atoms	15652
n_residues	2057
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	113.6 Å
rg_real	36.41 Å
rg_real_error	0.76 Å
i0_real	7.6160e+08
i0_real_error	1.1570e+07
rg_reciprocal	36.55 Å
i0_reciprocal	761700000.0000
total_estimate	0.8962
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	47.5 Å
skewness	0.171
kurtosis	-0.478
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	433300000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.926

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Benzoylformate decarboxylase
formula_weight	56645.0 kDa
ec_number	4.1.1.7
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	16874

MASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSPVKLE

Source

organism	Pseudomonas putida
ncbi_taxonomy_id	303
host_organism	Escherichia coli

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	30

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	11

Entity 4 non-polymer

description	THIAMINE DIPHOSPHATE
formula_weight	425.3 kDa
src_method	nat
entity_count	3

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	8

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1174

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6. Citations (1)

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length_a	97.690 Å
length_b	111.933 Å
length_c	199.637 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.250 Å
resolution_low	43.683 Å
r_factor	0.1902
r_work	0.1882
r_free	0.2290

fit	/app/data/saxs_computation/v6/9v67/9v67.fit
pddf	/app/data/pr_computation/v6/9v67/9v67.pr.out
profile	/app/data/saxs_computation/v6/9v67/9v67.dat