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10ps

Crystal structure of SdrD A2-A3-B1-B2 domains from Staphylococcus aureus JH1

Method: X-RAY DIFFRACTION D_max: 154.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10ps
deposition_date	2026-01-31
last_revision	2026-02-11
title	Crystal structure of SdrD A2-A3-B1-B2 domains from Staphylococcus aureus JH1
keywords	;SdrD, MSCRAMM, LPXTG-motif, Structural Genomics, PSI-Biology, Center for Structural Biology of Infectious Diseases, CSBID, CELL ADHESION ;; CELL ADHESION
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	38.59 Å
rg_electron	39.89 Å
i0	63153000.00
molecular_weight	61812.0 kDa
excluded_volume	76581 Å³
envelope_volume	109260 Å³
shell_volume	27296 Å³
envelope_diameter	161.2 Å
shell_rg	36.90 Å
envelope_rg	41.13 Å
shape_rg	39.89 Å
total_rg	39.67 Å
total_atoms	4333
n_residues	556
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	154.6 Å
rg_real	39.75 Å
rg_real_error	2.57 Å
i0_real	6.3150e+07
i0_real_error	1.3240e+06
rg_reciprocal	39.03 Å
i0_reciprocal	63110000.0000
total_estimate	0.6834
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	26.4 Å
skewness	0.784
kurtosis	0.042
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	3518000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.270; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.109; Smooth: 0.962

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Serine-aspartate repeat-containing protein D
formula_weight	61037.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4604

SNASKNVNDLITSNTTLTVVDADNSKTIVPAQDYLSLKSQITVDDKVKSGDYFTIKYSDTVQVYGLNPEDIKNIGDIKDPNNGETIATAKHDTANNLITYTFTDYVDRFNSVKMGINYSIYMDADTIPVDKKDVPFSVTIGNQITTTTADITYPAYKEADNNSIGSAFTETVSHVGNVEDPGYYNQVVYVNPMDKDLKGAKLKVEAYHPKYPTNIGQINQNVTNIKIYRVPEGYTLNKGYDVNTNDLVDVTDEFKNKMTYGSNQSVNLDFGDITSAYVVMVNTKFQYTNSESPTLVQMATLSSTGNKSVSTGNALGFTNNQSGGAGQEVYKIGNYVWEDTNKNGVQELGEKGVGNVTVTVFDNNTNTKVGEAVTKEDGSYLIPNLPNGDYRVEFSNLPKGYEVTPSKQGNNEELDSNGLSSVITVNGKDNLSADLGIYKPKYNLGDYVWEDTNKNGIQDQDEKGISGVTVTLKDENGNVLKTVTTDADGKYKFTDLDNGNYKVEFTTPEGYTPTTVTSGSDIEKDSNGLTTTGVINGADNMTLDSGFYKTPKYNLGNY

Source

organism	Staphylococcus aureus subsp. aureus JH1
ncbi_taxonomy_id	359787
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	9

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	7

Entity 5 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	3

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	256

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6. Citations (1)

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length_a	59.190 Å
length_b	58.570 Å
length_c	94.400 Å
angle_alpha	90.00 °
angle_beta	101.35 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.000 Å
resolution_low	27.100 Å
r_factor	0.2096
r_work	0.2084
r_free	0.2354

fit	/app/data/saxs_computation/0p/10ps/10ps.fit
pddf	/app/data/pr_computation/0p/10ps/10ps.pr.out
profile	/app/data/saxs_computation/0p/10ps/10ps.dat