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1d3c

MICHAELIS COMPLEX OF BACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN GLYCOSYLTRANSFERASE WITH GAMMA-CYCLODEXTRIN

Method: X-RAY DIFFRACTION D_max: 81.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d3c
deposition_date	1999-09-29
title	MICHAELIS COMPLEX OF BACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN GLYCOSYLTRANSFERASE WITH GAMMA-CYCLODEXTRIN
keywords	;ALPHA-AMYLASE, PRODUCT COMPLEX, OLIGOSACCHARIDE, FAMILY 13 GLYCOSYL HYDROLASE, TRANSGLYCOSYLATION, INDUCED FIT, CATALYSIS, TRANSFERASE ;; TRANSFERASE
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	26.79 Å
rg_electron	25.65 Å
i0	103868000.00
molecular_weight	79003.0 kDa
excluded_volume	98105 Å³
envelope_volume	111220 Å³
shell_volume	35139 Å³
envelope_diameter	84.8 Å
shell_rg	33.93 Å
envelope_rg	25.89 Å
shape_rg	25.62 Å
total_rg	26.52 Å
total_atoms	5562
n_residues	686
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	81.0 Å
rg_real	26.64 Å
rg_real_error	0.41 Å
i0_real	1.0390e+08
i0_real_error	1.2910e+06
rg_reciprocal	26.69 Å
i0_reciprocal	103900000.0000
total_estimate	0.9093
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	33.0 Å
skewness	0.174
kurtosis	-0.504
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	22080000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.951

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	CYCLODEXTRIN GLYCOSYLTRANSFERASE
formula_weight	74573.5 kDa
ec_number	2.4.1.19
mutation	D229N, E257Q
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6201

APDTSVSNKQNFSTDVIYQIFTDRFSDGNPANNPTGAAFDGTCTNLRLYCGGDWQGIINKINDGYLTGMGVTAIWISQPVENIYSIINYSGVNNTAYHGYWARDFKKTNPAYGTIADFQNLIAAAHAKNIKVIIDFAPNHTSPASSDQPSFAENGRLYDNGTLLGGYTNDTQNLFHHNGGTDFSTTENGIYKNLYDLADLNHNNSTVDVYLKDAIKMWLDLGIDGIRMNAVKHMPFGWQKSFMAAVNNYKPVFTFGQWFLGVNEVSPENHKFANESGMSLLDFRFAQKVRQVFRDNTDNMYGLKAMLEGSAADYAQVDDQVTFIDNHDMERFHASNANRRKLEQALAFTLTSRGVPAIYYGTEQYMSGGTDPDNRARIPSFSTSTTAYQVIQKLAPLRKCNPAIAYGSTQERWINNDVLIYERKFGSNVAVVAVNRNLNAPASISGLVTSLPQGSYNDVLGGLLNGNTLSVGSGGAASNFTLAAGGTAVWQYTAATATPTIGHVGPMMAKPGVTITIDGRGFGSSKGTVYFGTTAVSGADITSWEDTQIKVKIPAVAGGNYNIKVANAAGTASNVYDNFEVLSGDQVSVRFVVNNATTALGQNVYLTGSVSELGNWDPAKAIGPMYNQVVYQYPNWYYDVSVPAGKTIEFKFLKKQGSTVTWEGGSNHTFTAPSSGTATINVNWQP

Source

organism	Bacillus circulans
ncbi_taxonomy_id	1397
host_organism	Bacillus subtilis

Entity 2 branched

description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
formula_weight	342.3 kDa
src_method	man
entity_count	1

Entity 3 branched

description	Cyclooctakis-(1-4)-(alpha-D-glucopyranose)
formula_weight	1315.1 kDa
src_method	man
entity_count	3

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	(4S)-2-METHYL-2,4-PENTANEDIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	639

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6. Citations (4)

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length_a	117.791 Å
length_b	109.532 Å
length_c	65.223 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.780 Å
resolution_low	8.000 Å
r_factor	0.2220
r_work	0.2200
r_free	0.2580

fit	/app/data/saxs_computation/d3/1d3c/1d3c.fit
pddf	/app/data/pr_computation/d3/1d3c/1d3c.pr.out
profile	/app/data/saxs_computation/d3/1d3c/1d3c.dat