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1dki

CRYSTAL STRUCTURE OF THE ZYMOGEN FORM OF STREPTOCOCCAL PYROGENIC EXOTOXIN B ACTIVE SITE (C47S) MUTANT

Method: X-RAY DIFFRACTION D_max: 126.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dki
deposition_date	1999-12-07
title	CRYSTAL STRUCTURE OF THE ZYMOGEN FORM OF STREPTOCOCCAL PYROGENIC EXOTOXIN B ACTIVE SITE (C47S) MUTANT
keywords	ZYMOGEN, CYSTEINE PROTEASE, PAPAIN-LIKE, TOXIN; TOXIN
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	37.51 Å
rg_electron	37.37 Å
i0	311182000.00
molecular_weight	140420.0 kDa
excluded_volume	174260 Å³
envelope_volume	221510 Å³
shell_volume	50700 Å³
envelope_diameter	129.3 Å
shell_rg	42.39 Å
envelope_rg	37.00 Å
shape_rg	37.38 Å
total_rg	37.66 Å
total_atoms	9923
n_residues	1296
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	126.0 Å
rg_real	37.60 Å
rg_real_error	1.41 Å
i0_real	3.1120e+08
i0_real_error	5.6280e+06
rg_reciprocal	37.55 Å
i0_reciprocal	311200000.0000
total_estimate	0.8786
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	42.0 Å
skewness	0.396
kurtosis	-0.367
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	74470000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.840

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	PYROGENIC EXOTOXIN B ZYMOGEN
formula_weight	40318.5 kDa
mutation	C47S
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	10562

DQNFARNEKEAKDSAITFIQKSAAIKAGARSAEDIKLDKVNLGGELSGSNMYVYNISTGGFVIVSGDKRSPEILGYSTSGSFDVNGKENIASFMESYVEQIKENKKLDSTYAGTAEIKQPVVKSLLDSKGIHYNQGNPYNLLTPVIEKVKPGEQSFVGQHAATGSVATATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQYNWNNILPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKENFGYNQSVHQINRGDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVIDGADGRNFYHVNWGWGGVSDGFFRLDALNPSALGTGGGAGGFNGYQSAVVGIKP

Source

organism	Streptococcus pyogenes
ncbi_taxonomy_id	1314
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	639

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6. Citations (1)

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length_a	46.664 Å
length_b	116.556 Å
length_c	144.726 Å
angle_alpha	90.00 °
angle_beta	94.17 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.600 Å
resolution_low	30.000 Å
r_factor	0.2180
r_work	0.2180
r_free	0.2450

fit	/app/data/saxs_computation/dk/1dki/1dki.fit
pddf	/app/data/pr_computation/dk/1dki/1dki.pr.out
profile	/app/data/saxs_computation/dk/1dki/1dki.dat

CRYSTAL STRUCTURE OF THE ZYMOGEN FORM OF STREPTOCOCCAL PYROGENIC EXOTOXIN B ACTIVE SITE (C47S) MUTANT

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