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9v6f

The crystal structure of a ThDP-dependent enzyme PpBFD

Method: X-RAY DIFFRACTION D_max: 114.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v6f
deposition_date	2025-05-27
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	36.74 Å
rg_electron	35.82 Å
i0	734160000.00
molecular_weight	219590.0 kDa
excluded_volume	273870 Å³
envelope_volume	321280 Å³
shell_volume	70134 Å³
envelope_diameter	117.9 Å
shell_rg	45.08 Å
envelope_rg	36.01 Å
shape_rg	35.81 Å
total_rg	36.37 Å
total_atoms	15430
n_residues	2039
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	114.8 Å
rg_real	36.53 Å
rg_real_error	0.74 Å
i0_real	7.3420e+08
i0_real_error	1.1930e+07
rg_reciprocal	36.66 Å
i0_reciprocal	734300000.0000
total_estimate	0.8951
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.4 Å
skewness	0.174
kurtosis	-0.472
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	375500000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.940

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Benzoylformate decarboxylase
formula_weight	56677.1 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	15716

MASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEAFLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESLSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGGLRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSPVKLE

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	32

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	14

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	246

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6. Citations (1)

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length_a	95.734 Å
length_b	114.370 Å
length_c	202.158 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	2.639 Å
resolution_low	49.772 Å
r_factor	0.1926
r_work	0.1906
r_free	0.2305

fit	/app/data/saxs_computation/v6/9v6f/9v6f.fit
pddf	/app/data/pr_computation/v6/9v6f/9v6f.pr.out
profile	/app/data/saxs_computation/v6/9v6f/9v6f.dat