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1d0k

THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH TWO MURODIPEPTIDES (GLCNAC-MURNAC-L-ALA-D-GLU)

Method: X-RAY DIFFRACTION D_max: 82.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d0k
deposition_date	1999-09-12
title	THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH TWO MURODIPEPTIDES (GLCNAC-MURNAC-L-ALA-D-GLU)
keywords	ALPHA-HELICAL PROTEIN WITH A FIVE-STRANDED ANTIPARALLEL BETA-SHEET, GLYCOSYLTRANSFERASE, EF-HAND, 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	22.94 Å
rg_electron	21.97 Å
i0	23357100.00
molecular_weight	36626.0 kDa
excluded_volume	45661 Å³
envelope_volume	53907 Å³
shell_volume	21228 Å³
envelope_diameter	84.0 Å
shell_rg	27.96 Å
envelope_rg	22.54 Å
shape_rg	21.95 Å
total_rg	22.79 Å
total_atoms	2585
n_residues	314
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	82.6 Å
rg_real	23.03 Å
rg_real_error	0.82 Å
i0_real	2.3360e+07
i0_real_error	3.7000e+05
rg_reciprocal	23.01 Å
i0_reciprocal	23360000.0000
total_estimate	0.8420
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.1 Å
skewness	0.489
kurtosis	-0.092
angular_range	— – 0.3450 Å⁻¹
current_alpha	0.0000
highest_alpha	5906000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.695; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.870; Smooth: 0.988

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	35KD SOLUBLE LYTIC TRANSGLYCOSYLASE
formula_weight	36079.7 kDa
mutation	L40M, L41V
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3010

MVEPQHNVMQMGGDFANNPNAQQFIDKMVNKHGFDRQQLQEILSQAKRLDSVLRLMDNQAPTTSVKPPSGPNGAWLRYRKKFITPDNVQNGVVFWNQYEDALNRAWQVYGVPPEIIVGIIGVETRWGRVMGKTRILDALATLSFNYPRRAEYFSGELETFLLMARDEQDDPLNLKGSFAGAMGYGQFMPSSYKQYAVDFSGDGHINLWDPVDAIGSVANYFKAHGWVKGDQVAVMANGQAPGLPNGFKTKYSISQLAAAGLTPQQPLGNHQQASLLRLDVGTGYQYWYGLPNFYTITRYNHSTHYAMAVWQLGQAVALARVQ

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid
formula_weight	496.5 kDa
src_method	man
entity_count	2

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	ALANINE
formula_weight	89.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	D-GLUTAMIC ACID
formula_weight	147.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	362

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6. Citations (1)

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length_a	58.379 Å
length_b	67.825 Å
length_c	98.940 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	2.020 Å
resolution_low	20.000 Å
r_factor	0.1680
r_work	0.1650
r_free	0.2020

fit	/app/data/saxs_computation/d0/1d0k/1d0k.fit
pddf	/app/data/pr_computation/d0/1d0k/1d0k.pr.out
profile	/app/data/saxs_computation/d0/1d0k/1d0k.dat