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1dnl

;X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH FMN AT 1.8 ANGSTROM RESOLUTION ;

Method: X-RAY DIFFRACTION D_max: 68.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dnl
deposition_date	1999-12-16
title	;X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH FMN AT 1.8 ANGSTROM RESOLUTION ;
keywords	BETA BARREL, PROTEIN-FMN COMPLEX, OXIDOREDUCTASE; OXIDOREDUCTASE
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	20.33 Å
rg_electron	19.34 Å
i0	10898900.00
molecular_weight	23964.0 kDa
excluded_volume	29705 Å³
envelope_volume	36393 Å³
shell_volume	16567 Å³
envelope_diameter	69.1 Å
shell_rg	24.70 Å
envelope_rg	19.66 Å
shape_rg	19.36 Å
total_rg	20.11 Å
total_atoms	1678
n_residues	195
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	68.9 Å
rg_real	20.37 Å
rg_real_error	0.42 Å
i0_real	1.0900e+07
i0_real_error	1.1590e+05
rg_reciprocal	20.36 Å
i0_reciprocal	10900000.0000
total_estimate	0.8807
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	67.9 Å
skewness	0.406
kurtosis	-0.242
angular_range	— – 0.3900 Å⁻¹
current_alpha	0.0000
highest_alpha	2189000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.993

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	;PYRIDOXINE 5'-PHOSPHATE OXIDASE ;
formula_weight	23439.2 kDa
ec_number	1.4.3.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1824

GGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP

Source

organism	Escherichia coli K12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

Entity 2 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	FLAVIN MONONUCLEOTIDE
formula_weight	456.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	128

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6. Citations (1)

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length_a	63.710 Å
length_b	63.710 Å
length_c	125.250 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	—

resolution	1.800 Å
resolution_low	55.000 Å
r_factor	0.2120
r_work	0.2100
r_free	0.2330

fit	/app/data/saxs_computation/dn/1dnl/1dnl.fit
pddf	/app/data/pr_computation/dn/1dnl/1dnl.pr.out
profile	/app/data/saxs_computation/dn/1dnl/1dnl.dat

;X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH FMN AT 1.8 ANGSTROM RESOLUTION ;

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction