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9qj3

;Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and iodide at pH 5.5 ;

Method: X-RAY DIFFRACTION D_max: 117.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qj3
deposition_date	2025-03-18
title	;Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and iodide at pH 5.5 ;
keywords	Innate immunity, enzyme substrate complex, inhibitor, OXIDOREDUCTASE; OXIDOREDUCTASE
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	35.99 Å
rg_electron	35.28 Å
i0	497401000.00
molecular_weight	159720.0 kDa
excluded_volume	187850 Å³
envelope_volume	231040 Å³
shell_volume	53648 Å³
envelope_diameter	121.0 Å
shell_rg	42.63 Å
envelope_rg	35.30 Å
shape_rg	35.15 Å
total_rg	36.01 Å
total_atoms	10511
n_residues	1254
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	117.0 Å
rg_real	35.99 Å
rg_real_error	0.80 Å
i0_real	4.9740e+08
i0_real_error	7.6350e+06
rg_reciprocal	35.99 Å
i0_reciprocal	497400000.0000
total_estimate	0.6793
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	39.9 Å
skewness	0.351
kurtosis	-0.461
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	91050000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 0.101; Positv: 1.000; Valcen: 0.997; Smooth: 0.906

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Myeloperoxidase heavy chain
formula_weight	53321.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D
atom_count	10800

VNCETSCVQQPPCFPLKIPPNDPRIKNQADCIPFFRSCPACPGSNITIRNQINALTSFVDASMVYGSEEPLARNLRNMSNQLGLLAVNQRFQDNGRALLPFDNLHDDPCLLTNRSARIPCFLAGDTRSSEMPELTSMHTLLLREHNRLATELKSLNPRWDGERLYQEARKIVGAMVQIITYRDYLPLVLGPTAMRKYLPTYRSYNDSVDPRIANVFTNAFRYGHTLIQPFMFRLDNRYQPMEPNPRVPLSRVFFASWRVVLEGGIDPILRGLMATPAKLNRQNQIAVDEIRERLFEQVMRIGLDLPALNMQRSRDHGLPGYNAWRRFCGLPQPETVGQLGTVLRNLKLARKLMEQYGTPNNIDIWMGGVSEPLKRKGRVGPLLACIIGTQFRKLRDGDRFWWENEGVFSMQQRQALAQISLPRIICDNTGITTVSKNNIFMSNSYPRDFVNCSTLPALNLASWREAS

Entity 2 polymer

description	Myeloperoxidase light chain
formula_weight	12894.5 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C

VTCPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPAARASFVTG

Entity 3 polymer

description	Myeloperoxidase inhibitor SPIN
formula_weight	6922.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,F

ANFLEHELSYIDVLLDKNADQATKDNLRSYFADKGLHSIKDIINKAKQDGFDVSKYEHVK

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	4

Entity 5 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1098.0 kDa
src_method	man
entity_count	1

Entity 6 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1057.0 kDa
src_method	man
entity_count	1

Entity 7 non-polymer

description	IODIDE ION
formula_weight	126.9 kDa
src_method	syn
entity_count	89

Entity 8 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

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

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	273

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6. Citations (1)

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length_a	111.361 Å
length_b	111.361 Å
length_c	242.068 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	2.630 Å
resolution_low	101.170 Å
r_factor	0.1950
r_work	0.1922
r_free	0.2494

fit	/app/data/saxs_computation/qj/9qj3/9qj3.fit
pddf	/app/data/pr_computation/qj/9qj3/9qj3.pr.out
profile	/app/data/saxs_computation/qj/9qj3/9qj3.dat

;Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and iodide at pH 5.5 ;

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 (10)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 branched

Entity 6 branched

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)