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9w5z

Structure of heme transport protein Shr-Linker-NEAT1 from Streptococcus pyogenes in complex with heme.

Method: X-RAY DIFFRACTION D_max: 108.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w5z
deposition_date	2025-08-02
last_revision	2026-06-10
title	Structure of heme transport protein Shr-Linker-NEAT1 from Streptococcus pyogenes in complex with heme.
keywords	Heme binding Shr Streptococcus pyogenes Iron acquisition Antimicrobial strategy Heme transfer, METAL TRANSPORT; METAL TRANSPORT
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	29.97 Å
rg_electron	30.25 Å
i0	35529200.00
molecular_weight	46823.0 kDa
excluded_volume	58849 Å³
envelope_volume	77984 Å³
shell_volume	24230 Å³
envelope_diameter	110.9 Å
shell_rg	33.17 Å
envelope_rg	30.74 Å
shape_rg	30.23 Å
total_rg	30.61 Å
total_atoms	3284
n_residues	409
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	108.8 Å
rg_real	30.37 Å
rg_real_error	1.12 Å
i0_real	3.5530e+07
i0_real_error	6.2660e+05
rg_reciprocal	30.20 Å
i0_reciprocal	35520000.0000
total_estimate	0.7917
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.7 Å
skewness	0.638
kurtosis	-0.114
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	6157000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.632; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.504; Smooth: 0.888

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Streptococcal hemoprotein receptor
formula_weight	23174.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3361

STKLDVTTLEKAIKEADAIIAKESNKDAVKDLAEKLQVIKDSYKEIKDSKLLADTHRLLKDTIESYQAGEVSINNLTEGTYTLNFKANKENSEESSMLQGAFDKRAKLVVKADGTMEISMLNTALGQFLIDFSIESKGTYPAAVRKQVGQKDINGSYIRSEFTMPIDDLDKLHKGAVLVSAMGGQESDLNHYDKYTKLDMTFSKTVTKG

Source

organism	Streptococcus pyogenes
ncbi_taxonomy_id	1314
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	209.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	71

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6. Citations (1)

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length_a	42.585 Å
length_b	113.246 Å
length_c	44.281 Å
angle_alpha	90.00 °
angle_beta	96.44 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.350 Å
resolution_low	42.320 Å
r_factor	0.2182
r_work	0.2158
r_free	0.2642

fit	/app/data/saxs_computation/w5/9w5z/9w5z.fit
pddf	/app/data/pr_computation/w5/9w5z/9w5z.pr.out
profile	/app/data/saxs_computation/w5/9w5z/9w5z.dat

Structure of heme transport protein Shr-Linker-NEAT1 from Streptococcus pyogenes in complex with heme.

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