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1bui

Structure of the ternary microplasmin-staphylokinase-microplasmin complex: a proteinase-cofactor-substrate complex in action

Method: X-RAY DIFFRACTION D_max: 89.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1bui
deposition_date	1998-09-04
title	Structure of the ternary microplasmin-staphylokinase-microplasmin complex: a proteinase-cofactor-substrate complex in action
keywords	PLASMIN, STAPHYLOKINASE, SERINE PROTEINASE, FIBRINOLYSIS, COFACTOR, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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	25.69 Å
rg_electron	24.99 Å
i0	138696000.00
molecular_weight	62165.0 kDa
excluded_volume	60111 Å³
envelope_volume	99069 Å³
shell_volume	32446 Å³
envelope_diameter	92.2 Å
shell_rg	32.72 Å
envelope_rg	25.09 Å
shape_rg	25.01 Å
total_rg	25.57 Å
total_atoms	4704
n_residues	617
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	89.2 Å
rg_real	25.59 Å
rg_real_error	0.53 Å
i0_real	1.3870e+08
i0_real_error	1.9390e+06
rg_reciprocal	25.62 Å
i0_reciprocal	138700000.0000
total_estimate	0.8710
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	87.7 Å
skewness	0.217
kurtosis	-0.444
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	30860000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Plasminogen
formula_weight	27335.4 kDa
ec_number	3.4.21.7
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5017

AAPSFDCGKPQVEPKKCPGRVVGGCVAHPHSWPWQVSLRTRFGMHFCGGTLISPEWVLTAAHCLEKSPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDKVIPACLPSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIENKVCNRYEFLNGRVQSTELCAGHLAGGTDSCQGDSGGPLVCFEKDKYILQGVTSWGLGCARPNKPGVYVRVSRFVTWIEGVMRNN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Staphylokinase
formula_weight	14598.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

VLKGDDASYFEPTGPYLMVNVTGVDSKGNELLSPHYVEFPIKPGTTLTKEKIEYYVEWALDATAYKEFRVVELDPSAKIEVTYYDKNKKKEETKSFPITEKGFVVPDLSEHIKNPGFNLITKVVIEKK

Entity 3 non-polymer

description	L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide
formula_weight	395.9 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	313

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6. Citations (1)

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length_a	76.140 Å
length_b	76.140 Å
length_c	324.030 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	2.650 Å
resolution_low	10.000 Å
r_factor	0.2040
r_work	0.2040
r_free	0.2870

fit	/app/data/saxs_computation/bu/1bui/1bui.fit
pddf	/app/data/pr_computation/bu/1bui/1bui.pr.out
profile	/app/data/saxs_computation/bu/1bui/1bui.dat

Structure of the ternary microplasmin-staphylokinase-microplasmin complex: a proteinase-cofactor-substrate complex in action

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

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)