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10pa

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

Method: X-RAY DIFFRACTION D_max: 79.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10pa
deposition_date	2026-01-30
last_revision	2026-02-11
title	Crystal structure of SdrD A2-A3 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	24.02 Å
rg_electron	23.23 Å
i0	22061900.00
molecular_weight	35316.0 kDa
excluded_volume	43974 Å³
envelope_volume	54331 Å³
shell_volume	20579 Å³
envelope_diameter	82.0 Å
shell_rg	28.67 Å
envelope_rg	23.22 Å
shape_rg	23.21 Å
total_rg	24.01 Å
total_atoms	2476
n_residues	317
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	79.5 Å
rg_real	24.13 Å
rg_real_error	0.77 Å
i0_real	2.2060e+07
i0_real_error	3.4740e+05
rg_reciprocal	24.11 Å
i0_reciprocal	22060000.0000
total_estimate	0.6180
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	23.6 Å
skewness	0.456
kurtosis	-0.292
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	4895000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 0.994; Sysdev: 0.203; Positv: 1.000; Valcen: 0.903; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Serine-aspartate repeat-containing protein D
formula_weight	35394.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2574

SNASKNVNDLITSNTTLTVVDADNSKTIVPAQDYLSLKSQITVDDKVKSGDYFTIKYSDTVQVYGLNPEDIKNIGDIKDPNNGETIATAKHDTANNLITYTFTDYVDRFNSVKMGINYSIYMDADTIPVDKKDVPFSVTIGNQITTTTADITYPAYKEADNNSIGSAFTETVSHVGNVEDPGYYNQVVYVNPMDKDLKGAKLKVEAYHPKYPTNIGQINQNVTNIKIYRVPEGYTLNKGYDVNTNDLVDVTDEFKNKMTYGSNQSVNLDFGDITSAYVVMVNTKFQYTNSESPTLVQMATLSSTGNKSVSTGNALGFTNNQ

Source

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

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	98

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6. Citations (1)

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length_a	70.523 Å
length_b	73.148 Å
length_c	198.705 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 2 2 2
int_tables_number	23
crystal_system	orthorhombic

resolution	1.920 Å
resolution_low	36.570 Å
r_factor	0.2139
r_work	0.2121
r_free	0.2449

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