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1e4i

2-deoxy-2-fluoro-beta-D-glucosyl/enzyme intermediate complex of the beta-glucosidase from Bacillus polymyxa

Method: X-RAY DIFFRACTION D_max: 72.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e4i
deposition_date	2000-07-06
title	2-deoxy-2-fluoro-beta-D-glucosyl/enzyme intermediate complex of the beta-glucosidase from Bacillus polymyxa
keywords	HYDROLASE, FAMILY 1 GLYCOSYL HYDROLASE, COVALENT ENZYME-GLYCOSIDE INTERMEDIATE, ALPHA/BETA BARREL; HYDROLASE
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	22.21 Å
rg_electron	20.83 Å
i0	45673200.00
molecular_weight	52010.0 kDa
excluded_volume	64581 Å³
envelope_volume	71191 Å³
shell_volume	27188 Å³
envelope_diameter	70.9 Å
shell_rg	28.75 Å
envelope_rg	21.14 Å
shape_rg	20.81 Å
total_rg	21.75 Å
total_atoms	3679
n_residues	447
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	72.7 Å
rg_real	22.01 Å
rg_real_error	0.30 Å
i0_real	4.5670e+07
i0_real_error	4.9310e+05
rg_reciprocal	22.05 Å
i0_reciprocal	45670000.0000
total_estimate	0.8019
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.2 Å
skewness	0.079
kurtosis	-0.495
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	11570000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	BETA-GLUCOSIDASE
formula_weight	51566.6 kDa
ec_number	3.2.1.21
mutation	YES
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3913

TIFQFPQDFMWGTATAAYQIEGAYQEDGRGLSIWDTFAHTPGKVFNGDNGNVACDSYHRYEEDIRLMKELGIRTYRFSVSWPRIFPNGDGEVNQKGLDYYHRVVDLLNDNGIEPFCTLYHWDLPQALQDAGGWGNRRTIQAFVQFAETMFREFHGKIQHWLTFNEPWCIAFLSNMLGVHAPGLTNLQTAIDVGHHLLVAHGLSVRRFRELGTSGQIGIAPNVSWAVPYSTSEEDKAACARTISLHSDWFLQPIYQGSYPQFLVDWFAEQGATVPIQDGDMDIIGEPIDMIGINYYSMSVNRFNPEAGFLQSEEINMGLPVTDIGWPVESRGLYEVLHYLQKYGNIDIYITENGACINDEVVNGKVQDDRRISYMQQHLVQVHRTIHDGLHVKGYMAWSLLDNFEWAEGYNMRFGMIHVDFRTQVRTPKQSYYWYRNVVSNNWLETRR

Source

organism	BACILLUS POLYMYXA
ncbi_taxonomy_id	1406
host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

description	2-deoxy-2-fluoro-alpha-D-glucopyranose
formula_weight	182.1 kDa
src_method	man
entity_count	1

Entity 3 non-polymer

description	2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside
formula_weight	348.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	234

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6. Citations (2)

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length_a	136.230 Å
length_b	136.230 Å
length_c	173.260 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 4 2 2
int_tables_number	97
crystal_system	—

resolution	2.000 Å
resolution_low	8.000 Å
r_factor	0.2100
r_work	0.2100
r_free	0.2500

fit	/app/data/saxs_computation/e4/1e4i/1e4i.fit
pddf	/app/data/pr_computation/e4/1e4i/1e4i.pr.out
profile	/app/data/saxs_computation/e4/1e4i/1e4i.dat

2-deoxy-2-fluoro-beta-D-glucosyl/enzyme intermediate complex of the beta-glucosidase from Bacillus polymyxa

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