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1dee

Structure of S. aureus protein A bound to a human IgM Fab

Method: X-RAY DIFFRACTION D_max: 127.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dee
deposition_date	1999-11-15
title	Structure of S. aureus protein A bound to a human IgM Fab
keywords	;FAB-IBP COMPLEX CRYSTAL STRUCTURE 2.7A RESOLUTION BINDING OUTSIDE THE ANTIGEN COMBINING SITE SUPERANTIGEN FAB VH3 SPECIFICITY, IMMUNE SYSTEM ;; IMMUNE SYSTEM
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	42.47 Å
rg_electron	42.05 Å
i0	370886000.00
molecular_weight	154150.0 kDa
excluded_volume	191300 Å³
envelope_volume	267260 Å³
shell_volume	53445 Å³
envelope_diameter	128.3 Å
shell_rg	47.23 Å
envelope_rg	40.64 Å
shape_rg	42.04 Å
total_rg	42.36 Å
total_atoms	10849
n_residues	1416
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	127.8 Å
rg_real	42.30 Å
rg_real_error	0.90 Å
i0_real	3.7090e+08
i0_real_error	6.2010e+06
rg_reciprocal	42.47 Å
i0_reciprocal	371000000.0000
total_estimate	0.8432
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	55.3 Å
skewness	0.021
kurtosis	-0.771
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	17120000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.986; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	IGM RF 2A2
formula_weight	23343.8 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,C,E
atom_count	10859

DIQMTQSPSSLSASVGDRVTITCRTSQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSAPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Entity 2 polymer

description	IGM RF 2A2
formula_weight	24167.0 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,D,F

QVQLVESGGGVVQPGKSLRLSCAASGFTFSGYGMHWVRQAPGKGLEWVALISYDESNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKVKFYDPTAPNDYWGQGTLVTVSSGSASAPTLFPLVSCENSNPSSTVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPSKDVAQGTNEHVVCKVQHPNGNKEKDVPL

Entity 3 polymer

description	IMMUNOGLOBULIN G BINDING PROTEIN A
formula_weight	6103.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,H

FNKDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAPK

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Staphylococcus aureus

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	10

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6. Citations (1)

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length_a	68.520 Å
length_b	78.910 Å
length_c	163.240 Å
angle_alpha	90.00 °
angle_beta	100.71 °
angle_gamma	90.00 °
z_pdb	6

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.700 Å
resolution_low	10.000 Å
r_factor	0.2250
r_work	0.2170
r_free	0.2810

fit	/app/data/saxs_computation/de/1dee/1dee.fit
pddf	/app/data/pr_computation/de/1dee/1dee.pr.out
profile	/app/data/saxs_computation/de/1dee/1dee.dat

Structure of S. aureus protein A bound to a human IgM Fab

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

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)