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1bfd

BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA

Method: X-RAY DIFFRACTION D_max: 77.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1bfd
deposition_date	1998-04-30
title	BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
keywords	LYASE, CARBON-CARBON, DECARBOXYLASE, MANDELATE CATABOLISM, THIAMIN DIPHOSPHATE; LYASE
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	25.25 Å
rg_electron	24.14 Å
i0	53776600.00
molecular_weight	56307.0 kDa
excluded_volume	70177 Å³
envelope_volume	82904 Å³
shell_volume	28480 Å³
envelope_diameter	80.9 Å
shell_rg	31.65 Å
envelope_rg	24.35 Å
shape_rg	24.14 Å
total_rg	24.98 Å
total_atoms	3957
n_residues	523
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	77.6 Å
rg_real	25.16 Å
rg_real_error	0.36 Å
i0_real	5.3780e+07
i0_real_error	6.8480e+05
rg_reciprocal	25.19 Å
i0_reciprocal	53780000.0000
total_estimate	0.9119
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.3 Å
skewness	0.201
kurtosis	-0.571
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	10170000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.987

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	BENZOYLFORMATE DECARBOXYLASE
formula_weight	56402.7 kDa
ec_number	4.1.1.7
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4324

MASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSPVK

Source

organism	Pseudomonas putida
ncbi_taxonomy_id	303
host_organism	Escherichia coli

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	THIAMINE DIPHOSPHATE
formula_weight	425.3 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	346

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6. Citations (2)

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length_a	82.300 Å
length_b	96.600 Å
length_c	138.300 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 2 2 2
int_tables_number	23
crystal_system	—

resolution	1.600 Å
resolution_low	5.000 Å
r_factor	0.1520
r_work	0.1520
r_free	0.1860

fit	/app/data/saxs_computation/bf/1bfd/1bfd.fit
pddf	/app/data/pr_computation/bf/1bfd/1bfd.pr.out
profile	/app/data/saxs_computation/bf/1bfd/1bfd.dat