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9qjo

Structure of native leukocyte myeloperoxidase in complex with the Staphylococcal Peroxidase Inhibitor SPIN and bromide at pH 5.5

Method: X-RAY DIFFRACTION D_max: 115.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qjo
deposition_date	2025-03-19
title	Structure of native leukocyte myeloperoxidase in complex with the Staphylococcal Peroxidase Inhibitor SPIN and bromide 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	35.28 Å
rg_electron	34.84 Å
i0	409411000.00
molecular_weight	154850.0 kDa
excluded_volume	188890 Å³
envelope_volume	226650 Å³
shell_volume	52974 Å³
envelope_diameter	119.8 Å
shell_rg	42.34 Å
envelope_rg	35.07 Å
shape_rg	34.85 Å
total_rg	35.26 Å
total_atoms	10617
n_residues	1277
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	115.5 Å
rg_real	35.28 Å
rg_real_error	0.95 Å
i0_real	4.0940e+08
i0_real_error	6.7910e+06
rg_reciprocal	35.28 Å
i0_reciprocal	409400000.0000
total_estimate	0.8865
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	38.5 Å
skewness	0.360
kurtosis	-0.455
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	103600000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.932

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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	11121

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	8394.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,F

KVYSQNGLVLHDDANFLEHELSYIDVLLDKNADQATKDNLRSYFADKGLHSIKDIINKAKQDGFDVSKYEHVK

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	1

Entity 5 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	syn
entity_count	2

Entity 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	BROMIDE ION
formula_weight	79.9 kDa
src_method	syn
entity_count	56

Entity 8 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	nat
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	502

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6. Citations (1)

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length_a	110.878 Å
length_b	110.878 Å
length_c	240.703 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	2.180 Å
resolution_low	48.610 Å
r_factor	0.1808
r_work	0.1781
r_free	0.2324

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

Structure of native leukocyte myeloperoxidase in complex with the Staphylococcal Peroxidase Inhibitor SPIN and bromide 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 non-polymer

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)